ORCID Profile
0000-0001-5386-7925
Current Organisation
University of Queensland
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbial Ecology | Microbiology | Genomics | Genetics | Microbial Genetics | Bioinformatics | Biological Adaptation | Biologically active molecules | Optical Properties of Materials | Evolutionary Biology | Zoology | Synchrotrons; Accelerators; Instruments and Techniques | Microbiology not elsewhere classified | Gene Expression (incl. Microarray and other genome-wide approaches) | Environmental biotechnology | Vertebrate Biology | Animal Nutrition | Biodiscovery | Natural products and bioactive compounds | Biomedical Instrumentation | Environmental Technologies | Environmental Engineering | Inorganic Geochemistry | Population, Ecological and Evolutionary Genetics | Infectious Agents | Phylogeny and Comparative Analysis | Other Physical Sciences | Biodiscovery |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Application Software Packages (excl. Computer Games) | Plant Production and Plant Primary Products not elsewhere classified | Flora, Fauna and Biodiversity of environments not elsewhere classified | Forest and Woodlands Flora, Fauna and Biodiversity | Ecosystem Adaptation to Climate Change | Poultry | Documentation of Undescribed Flora and Fauna | Management of Solid Waste from Mineral Resource Activities | Beef Cattle | Dairy Cattle | Respiratory System and Diseases (incl. Asthma) | Infectious Diseases | Expanding Knowledge in Technology | Biofuel (Biomass) Energy | Rehabilitation of Degraded Mining Environments | Sheep - Meat | Expanding Knowledge in the Physical Sciences
Related Links
Publications
Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community
Publisher: American Society for Microbiology
Date: 10-2005
DOI: 10.1128/AEM.71.10.6319-6324.2005
Abstract: Analysis of assembled random shotgun sequence data from a low- ersity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm s le naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼10 6 cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Publisher: Oxford University Press (OUP)
Date: 20-08-2009
DOI: 10.1093/BIOINFORMATICS/BTP508
Abstract: Summary: Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between s les, both for in idual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes s led at multiple depths in the Pacific Ocean. Availability: shotgun.zool.gu.se Contact: dalevi@chalmers.se erik.kristiansson@zool.gu.se Supplementary information: supplementary data are available at Bioinformatics online.
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Publisher: Oxford University Press (OUP)
Date: 08-04-2004
DOI: 10.1093/BIOINFORMATICS/BTH226
Abstract: Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental s les but can be applied to other nucleotide sequence alignments. Availability: Bellerophon is available as an interactive web server at foo.maths.uq.edu.au/~huber/bellerophon.pl
Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes
Publisher: Springer Science and Business Media LLC
Date: 19-12-2016
DOI: 10.1038/SREP39114
Abstract: Three bioelectrochemical systems were operated with set anode potentials of +300 mV, +550 mV and +800 mV vs. Standard Hydrogen Electrode (SHE) to test the hypothesis that anode potential influences microbial ersity and is positively associated with microbial biomass and activity. Bacterial and archaeal ersity was characterized using 16 S rRNA gene licon sequencing, and biofilm thickness was measured as a proxy for biomass. Current production and substrate utilization patterns were used as measures of microbial activity and the mid-point potentials of putative terminal oxidases were assessed using cyclic voltammetry. All measurements were performed after 4, 16, 23, 30 and 38 days. Microbial biomass and activity differed significantly between anode potentials and were lower at the highest potential. Anodic electrode and electrolyte associated community composition was also significantly influenced by anode potential. While biofilms at +800 mV were thinner, transferred less charge and oxidized less substrate than those at lower potentials, they were also associated with putative terminal oxidases with higher mid-point potentials and generated more biomass per unit charge. This indicates that microbes at +800 mV were unable to capitalize on the potential for additional energy gain due to a lack of adaptive traits to high potential solid electron acceptors and/or sensitivity to oxidative stress.
Functional effects of the microbiota in chronic respiratory disease
Publisher: Elsevier BV
Date: 10-2019
Genome Project Standards in a New Era of Sequencing
Publisher: American Association for the Advancement of Science (AAAS)
Date: 09-10-2009
Abstract: More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
Publisher: Springer Science and Business Media LLC
Date: 15-10-2019
DOI: 10.1038/S41396-018-0282-Y
Abstract: Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniale s (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca . Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca . Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca . Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.
Roadmap for naming uncultivated Archaea and Bacteria
Publisher: Springer Science and Business Media LLC
Date: 08-06-2020
DOI: 10.1038/S41564-020-0733-X
Abstract: The assembly of single- lified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial ersity.
Metallo-beta-lactamase from Cronobacter sakazakii (Enterobacter sakazakii) HARLDQ motif mutant S60/R118H/Q121H/K254H
Publisher: Worldwide Protein Data Bank
Date: 19-06-2019
DOI: 10.2210/PDB6DR8/PDB
A catalogue of 136 microbial draft genomes from Red Sea metagenomes
Publisher: Springer Science and Business Media LLC
Date: 05-07-2016
Abstract: Earth is expected to continue warming and the Red Sea is a model environment for understanding the effects of global warming on ocean microbiomes due to its unusually high temperature, salinity and solar irradiance. However, most microbial ersity analyses of the Red Sea have been limited to cultured representatives and single marker gene analyses, hence neglecting the substantial uncultured majority. Here, we report 136 microbial genomes (completion minus contamination is ≥50%) assembled from 45 metagenomes from eight stations spanning the Red Sea and taken from multiple depths between 10 to 500 m. Phylogenomic analysis showed that most of the retrieved genomes belong to seven different phyla of known marine microbes, but more than half representing currently uncultured species. The open-access data presented here is the largest number of Red Sea representative microbial genomes reported in a single study and will help facilitate future studies in understanding the physiology of these microorganisms and how they have adapted to the relatively harsh conditions of the Red Sea.
A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities
Publisher: Springer Science and Business Media LLC
Date: 28-08-2017
DOI: 10.1038/S41564-017-0010-9
Abstract: Microbial interactions influence the productivity and biogeochemistry of the ocean, yet they occur in miniscule volumes that cannot be s led by traditional oceanographic techniques. To investigate the behaviours of marine microorganisms at spatially relevant scales, we engineered an in situ chemotaxis assay (ISCA) based on microfluidic technology. Here, we describe the fabrication, testing and first field results of the ISCA, demonstrating its value in accessing the microbial behaviours that shape marine ecosystems.
Parameter Estimation and Species Tree Rooting Using ALE and GeneRax
Publisher: Oxford University Press (OUP)
Date: 07-2023
DOI: 10.1093/GBE/EVAD134
Abstract: ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root in Bacteria—where there is less certainty about the root position—ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.
Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)
Publisher: Springer Science and Business Media LLC
Date: 07-2011
DOI: 10.4056/SIGS.2004648
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Publisher: PeerJ
Date: 22-09-2016
DOI: 10.7717/PEERJ.2486
Abstract: High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass s les. Current methods for lifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically erse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume s les, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal
Publisher: Springer Science and Business Media LLC
Date: 25-07-2013
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2019
DOI: 10.1101/762682
Abstract: Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to in idual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.
PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues
Publisher: Elsevier BV
Date: 02-2003
DOI: 10.1016/S0378-1135(02)00291-2
Abstract: The polymerase chain reaction (PCR) was used to lify specific segments of the 16S ribosomal RNA gene of Clostridium chauvoei, a major pathogen of ruminants. Three sets of primers were used to produce licons of 159, 836 and 959 base pairs (bp), respectively. The PCR was evaluated by testing clinically important strains of Clostridium, including 21 strains of C. chauvoei, five strains each of Clostridium septicum and Clostridium perfringens and two strains each of Clostridium novyi, Clostridium histolyticum and Clostridium sordellii. Both purified DNA and biomass from pure cultures of each of these microorganisms were evaluated as templates in the PCR. In addition, extracts of formalin-fixed, paraffin-embedded tissues of eight sheep experimentally inoculated with C. chauvoei or C. septicum (four animals each) were also tested by the PCR using the three sets of primers. Purified DNA template of all C. chauvoei strains produced PCR licons of the expected size for all three primer pairs. However, when biomass from pure cultures of C. chauvoei or tissue extracts were used as templates, only the primer pair designed to produce the 159bp licon gave consistently positive results. No positive results were obtained with any primer pair when purified DNA or biomass from pure cultures of non-target clostridial species were used as templates. Therefore, the PCR primer sets appear to be very specific for identifying C. chauvoei in both cultures and tissues.
Multiple displacement amplification compromises quantitative analysis of metagenomes
Publisher: Springer Science and Business Media LLC
Date: 29-11-2010
Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
Publisher: Cold Spring Harbor Laboratory
Date: 03-03-2020
DOI: 10.1101/2020.03.01.972265
Abstract: An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary ergence (RED). The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios, and expansion of the genome database. Rank normalization was shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the former Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. The taxonomy is publicly available at the GTDB website ( gtdb.ecogenomic.org ).
Laboratory Cultivation of Widespread and PreviouslyUncultured SoilBacteria
Publisher: American Society for Microbiology
Date: 12-2003
DOI: 10.1128/AEM.69.12.7210-7215.2003
Abstract: Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. They included members of sub isions 1, 2, 3, and 4 of the phylum Acidobacteria , sub ision 3 of the phylum Verrucomicrobia , sub ision 1 of the phylum Gemmatimonadetes , and subclasses Acidimicrobidae and Rubrobacteridae of the phylum Actinobacteria . In addition, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum Actinobacteria and classes Alphaproteobacteria , Betaproteobacteria , and Gammaproteobacteria of the phylum Proteobacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called unculturable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel soil bacteria.
Correlative TEM and FISH Imaging of Microbial Communities
Publisher: Oxford University Press (OUP)
Date: 07-2009
DOI: 10.1017/S1431927609098250
Abstract: Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
Grinder: a versatile amplicon and shotgun sequence simulator
Publisher: Oxford University Press (OUP)
Date: 19-03-2012
DOI: 10.1093/NAR/GKS251
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life (vol 2, pg 1533, 2017)
Publisher: Springer Science and Business Media LLC
Date: 12-12-2018
DOI: 10.1038/S41564-017-0083-5
Abstract: In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806-8811 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota represents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum. This has now been corrected in all versions of the Article. An updated version of Fig. 5 has also been used to replace the previous version, with the row for Parvarchaeota removed, and Supplementary Table 15 and Supplementary Table 17 have both been replaced to reflect the availability of the two additional Parvarchaeota genomes. In addition, the Methods incorrectly stated that all metagenomes identified as being from studies where MAGs had previously been recovered were excluded from consideration. Metagenomes from studies where MAGs had previously been recovered were retained if the UBA MAGs provided appreciable improvements in genome quality or phylogenetic ersity. All versions of the Article have been updated to indicate the retention of such metagenomes.
Yeast as a Biofertilizer Alters Plant Growth and Morphology
Publisher: Wiley
Date: 03-2014
Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae
Publisher: Springer Science and Business Media LLC
Date: 26-03-2003
DOI: 10.1007/S00203-003-0528-5
Abstract: The component bacteria of a three-membered mixed culture able to ferment glycolate to acetate, propionate and CO(2) were isolated in pure culture. All three strains were strict anaerobes that, on the basis of comparative 16S rRNA gene sequence analysis, belonged to the order Clostridiales in the phylum Firmicutes (low G+C gram-positive bacteria). Two of the strains were not involved in glycolate metabolism. The third, the glycolate-fermenting strain 19gly4 (DSM 11261), was related to members of the family Lachnospiraceae. The cells of strain 19gly4 were oval- to lemon-shaped, 0.85 microm long and 0.65 microm in diameter, occurring singly, in pairs, or in chains of up to 30 cells. Strain 19gly4 fermented glycolate or fumarate to acetate, succinate, and CO(2). Hydrogen was not formed, and strain 19gly4 was able to grow on glycolate in pure culture without any syntrophic hydrogen transfer and without the use of an external electron acceptor. There was no evidence for homoacetogenic metabolism. This bacterium therefore differs in metabolism from previously reported glycolate-utilising anaerobes.
Su1204 VARIATIONS OF THE MUCOSA ASSOCIATED MICROBIOTA ALONG THE HUMAN GASTROINTESTINAL TRACT IN HEALTH AND INFLAMMATORY BOWEL DISEASE
Publisher: Elsevier BV
Date: 05-2020
An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event
Publisher: Cold Spring Harbor Laboratory
Date: 11-08-2023
DOI: 10.1101/2023.08.08.552427
Abstract: Most of life’s ersity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ∼2.33 billion years ago (Ga, (Poulton et al. 2021)), in which oxygenic photosynthesis and tectonism (Eguchi, Seales, and Dasgupta 2019) transformed Earth’s biosphere from dominantly anaerobic to aerobic. Here, we combine machine learning and phylogenetic reconciliation to infer ancestral transitions to aerobic lifestyles during bacterial evolution. Linking these transitions to the GOE provides new constraints to infer the timetree of Bacteria. We find that extant bacterial phyla are truly ancient, having radiated in the Archaean and the Proterozoic: the oldest include Bacillota (Firmicutes), which radiated 3.1-3.7 Ga, Cyanobacteria (3.3-3.5 Ga) and Patescibacteria (3-3.5 Ga). We show that most bacterial phyla were ancestrally anaerobic and that most transitions to an aerobic lifestyle post-dated the GOE. Our analyses trace oxygen production and consumption back to Cyanobacteria. From that starting point, horizontal transfer seeded aerobic lifestyles across bacterial ersity over hundreds of millions of years. Our analyses demonstrate that the ersification of aerobes proceeded in two waves corresponding to the GOE and to a second sustained rise in atmospheric O 2 at the dawn of the Palezoic (Krause et al. 2022).
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts
Publisher: Springer Science and Business Media LLC
Date: 06-08-2022
DOI: 10.1038/S41396-022-01298-5
Abstract: Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H 2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly ( p 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota , Firmicutes , Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic ersity within RuBisCO form IE ( rbcL1E ), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage (Nature (2013) 500 (567-570) doi:10.1038/nature12375)
Publisher: Springer Science and Business Media LLC
Date: 09-2013
DOI: 10.1038/NATURE12619
Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing
Publisher: Springer Science and Business Media LLC
Date: 08-05-2020
DOI: 10.1038/S41598-020-64761-3
Abstract: Microorganisms employ quorum sensing (QS) mechanisms to communicate with each other within microbial ecosystems. Emerging evidence suggests that intraspecies and interspecies QS plays an important role in antimicrobial resistance in microbial communities. However, the relationship between interkingdom QS and antimicrobial resistance is largely unknown. Here, we demonstrate that interkingdom QS interactions between a bacterium, Pseudomonas aeruginosa and a yeast, Candida albicans , induce the resistance of the latter to a widely used antifungal fluconazole. Phenotypic, transcriptomic, and proteomic analyses reveal that P. aeruginosa’s main QS molecule, N-(3-Oxododecanoyl)-L-homoserine lactone, induces candidal resistance to fluconazole by reversing the antifungal’s effect on the ergosterol biosynthesis pathway. Accessory resistance mechanisms including upregulation of C. albicans drug-efflux, regulation of oxidative stress response, and maintenance of cell membrane integrity, further confirm this phenomenon. These findings demonstrate that P. aeruginosa QS molecules may confer protection to neighboring yeasts against azoles, in turn strengthening their co-existence in hostile polymicrobial infection sites.
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
Publisher: Springer Science and Business Media LLC
Date: 27-05-2010
Abstract: We modified the standard ribosomal RNA-targeted fluorescence in situ hybridization (FISH) protocol by removing the fixation steps to allow recovery of unmodified nucleic acids. Using this method, hybridized cells could be visualized in two bioreactor sludges and termite hindgut s les by epifluorescence microscopy. We then targeted one bacterial and one archaeal population in the sludge s les with group-specific oligonucleotide probes using in-solution fixation-free FISH and sorted hybridized populations using fluorescence-activated cell sorting (FACS). We could show that sorted populations were highly enriched for the target organisms based on 16S rRNA gene sequencing, thus confirming probe specificity using the modified FISH protocol. This approach should facilitate subsequent genomic sequencing and analysis of targeted populations as DNA is not compromised by crosslinking during fixation.
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Publisher: Springer Science and Business Media LLC
Date: 2007
Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif
Publisher: Worldwide Protein Data Bank
Date: 19-06-2019
DOI: 10.2210/PDB6DQH/PDB
GroopM: an automated tool for the recovery of population genomes from related metagenomes
Publisher: PeerJ
Date: 30-09-2014
DOI: 10.7717/PEERJ.603
Back from the dead; the curious tale of the predatory cyanobacteriumVampirovibrio chlorellavorus
Publisher: PeerJ
Date: 21-05-2015
DOI: 10.7717/PEERJ.968
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin‐containing enzymes
Publisher: Wiley
Date: 06-2002
DOI: 10.1046/J.1365-2958.2002.02978.X
Abstract: Dimethyl sulphide dehydrogenase catalyses the oxidation of dimethyl sulphide to dimethyl sulphoxide (DMSO) during photoautotrophic growth of Rhodovulum sulfidophilum. Dimethyl sulphide dehydrogenase was shown to contain bis(molybdopterin guanine dinucleotide)Mo, the form of the pterin molybdenum cofactor unique to enzymes of the DMSO reductase family. Sequence analysis of the ddh gene cluster showed that the ddhA gene encodes a polypeptide with highest sequence similarity to the molybdopterin-containing subunits of selenate reductase, ethylbenzene dehydrogenase. These polypeptides form a distinct clade within the DMSO reductase family. Further sequence analysis of the ddh gene cluster identified three genes, ddhB, ddhD and ddhC. DdhB showed sequence homology to NarH, suggesting that it contains multiple iron-sulphur clusters. Analysis of the N-terminal signal sequence of DdhA suggests that it is secreted via the Tat secretory system in complex with DdhB, whereas DdhC is probably secreted via a Sec-dependent mechanism. Analysis of a ddhA mutant showed that dimethyl sulphide dehydrogenase was essential for photolithotrophic growth of Rv. sulfidophilum on dimethyl sulphide but not for chemo-trophic growth on the same substrate. Mutational analysis showed that cytochrome c2 mediated photosynthetic electron transfer from dimethyl sulphide dehydrogenase to the photochemical reaction centre, although this cytochrome was not essential for photoheterotrophic growth of the bacterium.
An evolving view of methane metabolism in the Archaea
Publisher: Springer Science and Business Media LLC
Date: 21-01-2019
DOI: 10.1038/S41579-018-0136-7
Abstract: Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth's climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and ergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the ersity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
Publisher: Springer Science and Business Media LLC
Date: 13-03-2021
DOI: 10.1038/S41396-021-00988-W
Abstract: Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene licon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and s ling date. Several taxa were highly abundant and prevalent in all s les, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Publisher: Springer Science and Business Media LLC
Date: 18-06-2018
DOI: 10.1038/NMICROBIOL.2016.170
Abstract: Methanogenesis is the primary biogenic source of methane in the atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within the Euryarchaeota was recently challenged by the discovery of putative methane-metabolizing genes in members of the Bathyarchaeota, suggesting that methanogenesis may be more phylogenetically widespread than currently appreciated. Here, we present the discovery of ergent methyl-coenzyme M reductase genes in population genomes recovered from anoxic environments with high methane flux that belong to a new archaeal phylum, the Verstraetearchaeota. These archaea encode the genes required for methylotrophic methanogenesis, and may conserve energy using a mechanism similar to that proposed for the obligate H 2 -dependent methylotrophic Methanomassiliicoccales and recently described Candidatus ‘Methanofastidiosa’. Our findings indicate that we are only beginning to understand methanogen ersity and support an ancient origin for methane metabolism in the Archaea, which is changing our understanding of the global carbon cycle.
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017)
Publisher: Frontiers Media SA
Date: 18-04-2018
Accurate phylogenetic classification of variable-length DNA fragments
Publisher: Springer Science and Business Media LLC
Date: 10-12-2006
DOI: 10.1038/NMETH976
Abstract: Metagenome studies have retrieved vast amounts of sequence data from a variety of environments leading to new discoveries and insights into the uncultured microbial world. Except for very simple communities, the encountered ersity has made fragment assembly and the subsequent analysis a challenging problem. A taxonomic characterization of metagenomic fragments is required for a deeper understanding of shotgun-sequenced microbial communities, but success has mostly been limited to sequences containing phylogenetic marker genes. Here we present PhyloPythia, a composition-based classifier that combines higher-level generic clades from a set of 340 completed genomes with s le-derived population models. Extensive analyses on synthetic and real metagenome data sets showed that PhyloPythia allows the accurate classification of most sequence fragments across all considered taxonomic ranks, even for unknown organisms. The method requires no more than 100 kb of training sequence for the creation of accurate models of s le-specific populations and can assign fragments >or=1 kb with high specificity.
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Publisher: Springer Science and Business Media LLC
Date: 17-12-2019
DOI: 10.1038/NBT.4306
The development and use of real-time PCR for the quantification of nitrifiers in activated sludge
Publisher: IWA Publishing
Date: 07-2002
Abstract: Chemical analytical data has long been used to monitor the performance of activated sludge plants even though the process relies on the performance of microorganisms. It is now evident that a rapid and reliable quantitative method is required, to be able to monitor the organisms responsible for nutrient transformation and their activities, allowing avenues for more efficient nutrient removal. The development of real-time or quantitative polymerase chain reaction (PCR) also known as TaqMan® or 5′-nuclease assay has allowed the rapid, quantitative analysis of DNA templates, eliminating some of the variability traditionally associated with other quantitative techniques. In this study analysis of Nitrospira spp., one of the key organisms in nitrite oxidation in wastewater treatment, was used to validate real-time PCR for the their quantification in activated sludge. A probe and primer set, targeting the 16S rRNA gene of Nitrospira spp. was designed according to the constraints of the TaqMan® specifications. S les used to evaluate the method included DNA from the sludge from full-scale wastewater treatment plants and laboratory scale systems. The reproducibility, quantitative efficiency and specificity were assessed in the evaluation. It was concluded that the method is sensitive and reproducible but has some constraints on the quantitative efficiency. A survey of full-scale systems for Nitrospira spp. was carried out and the results are presented here.
Link scientific publications using linked data
Publisher: IEEE
Date: 02-2015
Evolution of photosynthesis and aerobic respiration in the cyanobacteria
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.FREERADBIOMED.2019.03.029
Abstract: For well over a hundred years, members of the bacterial phylum Cyanobacteria have been considered strictly photosynthetic microorganisms, reflected in their classification as "blue-green algae" in the botanical code. Recently, genomes recovered from environmental sequencing surveys representing two major uncultured basal lineages (classes) of Cyanobacteria have been found to completely lack photosynthetic and CO
Author Correction: Greengenes2 unifies microbial data in a single reference tree
Publisher: Springer Science and Business Media LLC
Date: 18-10-2023
The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity
Publisher: Oxford University Press (OUP)
Date: 04-1997
DOI: 10.1046/J.1365-2672.1997.00111.X
Abstract: Five isolates of a filamentous bacterial morphotype with the distinctive diagnostic microscopic features of Eikelboom Type 1863 were obtained from activated sludge sewage treatment plants in Victoria, Australia. On the basis of phenotypic evidence and 16S rDNA sequence data, these isolates proved to be polyphyletic. Two (Ben 06 and Ben 06C) are from the Chryseobacterium subgroup which is in the Cytophaga group, sub ision I of the Flexibacter-Cytophaga-Bacteroides phylum. Two (Ben 56 and Ben 59) belong to the genus Acinetobacter, and one (Ben 58) is a Moraxella sp., closest to Mor. osloensis. The significance of these findings to the reliance on microscopic features for identification of these filamentous bacteria in activated sludge is discussed.
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation‐independent surveys
Publisher: Wiley
Date: 11-2002
DOI: 10.1046/J.1462-2920.2002.00352.X
Abstract: The culturability of microorganisms in a 10 cm core of an Australian pasture soil was investigated using a minimal agar medium with xylan as the growth substrate. Culturability decreased with increasing depth, from a maximum of 19% of the total microscopically countable cells in the 0-2 cm section to 2.4% in the 8-10 cm section. Seventy-one isolates from the core were identified by comparative 16S rRNA gene sequence analysis. Many of these isolates belong to groups of globally distributed soil bacteria, including well-characterized families of the classes Alphaproteobacteria and Betaproteobacteria, and of the subclass Actinobacteridae. Other isolates belong to groups with few or no cultivated representatives: 10 isolates in two sub isions of the phylum Acidobacteria, five isolates in a new order and nine isolates in a new family of the class Alphaproteobacteria, two isolates in a new order of the class Gammaproteobacteria, three isolates in two new families of the subclass Actinobacteridae, and two isolates in the subclass Rubrobacteridae. These new isolates represent the first laboratory cultures able to be assigned to some of these groups and greatly increase the number of cultivated strains known for others. This demonstrates that a minimal change in cultivation strategy (using a polymeric growth substrate and longer incubation times) can result in the isolation of globally distributed but previously uncultured phylogenetically novel soil bacteria.
Critical evaluation of faecal microbiome preservation using metagenomic analysis
Publisher: Springer Science and Business Media LLC
Date: 05-05-2021
DOI: 10.1038/S43705-021-00014-2
Abstract: The ability to preserve microbial communities in faecal s les is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal s les, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal s les from five participants, totalling 180 s les. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 s les across 10 in iduals after storage at −20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
Changes in the Gut Microbiome in Chronic Obstructive Pulmonary Disease
Publisher: American Thoracic Society
Date: 05-2020
DOI: 10.1164/AJRCCM-CONFERENCE.2020.201.1_MEETINGABSTRACTS.A4473
A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification
Publisher: Elsevier BV
Date: 03-1994
Genome Taxonomy Database and SeqCode: Microbial Taxonomy and Nomenclature in the Age of Big Sequence Data
Publisher: Pensoft Publishers
Date: 16-08-2023
Abstract: Microbial taxonomy and nomenclature have been challenged by methodological advances in high-throughput sequencing and high-performance computing. While taxonomy appears to adapt rapidly and has benefited enormously from the availability of whole-genome sequences, nomenclature still struggles to embrace these changes. Here, we present two independent initiatives that have resulted from the transitions of taxonomic practices in microbiology from a phenotypic and single gene-driven framework to a genome-based driven framework. The first initiative, the Genome Taxonomy Database (GTDB), was developed to address the needs of microbial taxonomists to classify rapidly accumulating genome sequences from both cultured and uncultured microorganisms. Availability of growing numbers of metagenome-assembled genomes (MAGs) and single lified genomes (SAGs), combined with the genomes from cultured species, created a perfect opportunity for building a consensus classification based on an evolutionary framework. This has been realised in the GTDB, a knowledgebase that provides phylogenetically consistent and rank-normalised taxonomies for bacterial and archaeal genomes. A distinctive feature of GTDB is a complete classification of genomes from species to domain using an automated approach combining average nucleotide identity (ANI) and relative evolutionary ergence (RED), followed by manual curation. GTDB has become an essential taxonomic resource for microbiologists worldwide, attracting ~3,500 users per month. GTDB mainly relies on two public databases, the National Center for Biotechnology Information (NCBI) Assembly database to which GTDB releases are indexed and the List of Prokaryotic names with Standing in Nomenclature (LPSN), as the primary nomenclatural reference. The database operates according to the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and incorporates its own internal (e.g., standards for delineating taxa) as well as external standards. The latter are often directly adopted from the NCBI since it is used as a primary source of genomes as well as metadata. Ex les of such standards include Darwin Core data standards from Bio ersity Information Standards (TDWG), Minimum Information (MI) about any (x) Sequence (MIxS) and MISAG and MIMAG standards (Bowers et al. 2017) from the Genomic Standards Consortium. GTDB is used by many third-party resources and provides direct links to external public resources used for curation and validation of taxonomies. Importantly, GTDB contributes to the further generation of knowledge by enabling users to classify their own genomes within the GTDB taxonomic framework using our open-source GTDB-Tk tool. To our knowledge, GTDB is the only database that provides a comprehensive systematic de novo taxonomy for prokaryotes, which serves a multitude of purposes to its global users. The second initiative, the Code of Nomenclature of Prokaryotes Described from Sequence Data or SeqCode, was developed in response to the need for formal naming of uncultured microbial ersity. This need has become even more evident with the establishment of the GTDB taxonomy, which highlighted many issues with nomenclature of uncultured taxa at scale. These include the absence of nomenclatural types, proposed higher taxon names without named children, and the lack of priority for Candidatus names (a prefix indicating a provisional status for the names of organisms falling outside the existing Prokaryotic Code). All these issues arise from one core issue: the absence of regulations for naming uncultured taxa because the International Code of Nomenclature of Prokaryotes (ICNP Oren et al. 2023) only applies to microorganisms able to be obtained in pure culture. To solve this problem and ultimately to be able to express taxonomic affiliations of uncultured taxa in a regulated manner, genome sequences are proposed to serve as nomenclatural types under the SeqCode. This new code has many common aspects with the ICNP and recognises names that are validly published under the ICNP. It operates via an online Registry that allows registration and validation of names following one of two paths: new names are registered and reviewed prior to publication and validated upon the notification about effective publication, or existing names such as names of Candidatus taxa are registered and reviewed with a validation certificate granted upon the satisfaction of all checks. new names are registered and reviewed prior to publication and validated upon the notification about effective publication, or existing names such as names of Candidatus taxa are registered and reviewed with a validation certificate granted upon the satisfaction of all checks. To avoid naming ambiguity and ensure accurate species descriptions, SeqCode requires that genome sequences designated as types satisfy recommendations on minimal standards for DNA sequences, which are largely adopted from the MISAG and MIMAG standards. The SeqCode Registry also embraces FAIR principles, and was developed with interoperable data structures to facilitate the sharing of its names across global bio ersity resources including GTDB. Recently, we illustrated how SeqCode can be applied, along with the ICNP, by proposing new names for GTDB-defined higher taxonomic names under the two codes (Chuvochina et al. 2023). While it is not ideal to operate under two Prokaryotic codes, we believe that this development is a necessary step towards a unified nomenclatural system.
First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community
Publisher: Elsevier BV
Date: 08-2020
Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid
Publisher: American Chemical Society (ACS)
Date: 05-04-2018
Abstract: Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.
68 Distinct Microbial Signatures of Healthy and Failing Lung Allografts
Publisher: Elsevier BV
Date: 04-2012
Unlocking the potential of metagenomics through replicated experimental design
Publisher: Springer Science and Business Media LLC
Date: 06-2012
DOI: 10.1038/NBT.2235
Correction
Publisher: Informa UK Limited
Date: 27-02-2020
Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type
Publisher: Elsevier BV
Date: 09-2022
16S rRNA analysis of isolates obtained from Gram-negative, filamentous bacteria micromanipulated from activated sludge
Publisher: Elsevier BV
Date: 10-1996
Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota
Publisher: Springer Science and Business Media LLC
Date: 24-01-2022
Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database
Publisher: Oxford University Press (OUP)
Date: 28-09-2021
Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57
Publisher: Oxford University Press (OUP)
Date: 06-02-2018
DOI: 10.1111/JAM.13688
Abstract: The probiotic Bacillus amyloliquefaciens H57 increased weight gain, increased nitrogen retention and increased feed intake in ruminants when administered to the diet. This study aims to develop a better understanding of this probiotic effect by analysing changes in the rumen prokaryotic community. Sequencing the 16S rRNA gene PCR licons of the rumen microbiome, revealed that ewes fed H57 had a significantly different rumen microbial community structure to Control sheep. In contrast, dairy calves showed no significant differences in rumen community structure between treatment groups. In both instances, H57 was below detection in the rumen community profile and was only present at low relative abundance as determined by qPCR. The altered rumen microbial community in sheep likely contributes to increased weight gain through more efficient digestion of plant material. As no change occurred in the rumen community of dairy calves it is suggested that increased weight gain may be due to changes in community function rather than structure. The low relative abundance of H57 as determined by qPCR, suggests that weight gain was not directly mediated by the probiotic, but rather by influencing animal behaviour (feed consumption) and/or altering the native rumen community structure or function. This study provides a novel look at the rumen prokaryotic community in both sheep and dairy calves when fed H57. These findings improve our understanding for the potential rumen community involvement in H57-enabled weight gain. The study reveals that the probiotic B. amyloliquefaciens H57 is capable of benefiting ruminants without colonizing the rumen, suggesting an indirect mechanism of action.
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
Publisher: Public Library of Science (PLoS)
Date: 11-04-2013
Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. n
Publisher: Microbiology Society
Date: 07-2003
Abstract: A phylogenetically novel aerobic bacterium was isolated from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a gram-negative, rod-shaped aerobe. Cells often appeared to ide by budding replication. Strain T-27T grew at 25-35 degrees C with an optimum growth temperature of 30 degrees C, whilst no growth was observed below 20 degrees C or above 37 degrees C within 20 days incubation. The pH range for growth was 6.5-9.5, with an optimum at pH 7.0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15:0, C16:1 and C14:0. The G + C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate ision BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19% 16S rDNA sequence ergence) that is greater than well-known phyla such as the Actinobacteria (18% ergence).
Probiotic Bifidobacterium longum subsp. longum Protects against Cigarette Smoke-Induced Inflammation in Mice
Publisher: MDPI AG
Date: 23-12-2023
DOI: 10.3390/IJMS24010252
Abstract: Bifidobacterium are prominent gut commensals that produce the short-chain fatty acid (SCFA) acetate, and they are often used as probiotics. Connections between the gut and the lung, termed the gut–lung axis, are regulated by the microbiome. The gut–lung axis is increasingly implicated in cigarette smoke-induced diseases, and cigarette smoke exposure has been associated with depletion of Bifidobacterium species. In this study, we assessed the impact of acetate-producing Bifidobacterium longum subsp. longum (WT) and a mutant strain with an impaired acetate production capacity (MUT) on cigarette smoke-induced inflammation. The mice were treated with WT or MUT B. longum subsp. longum and exposed to cigarette smoke for 8 weeks before assessments of lung inflammation, lung tissue gene expression and cecal SCFAs were performed. Both strains of B. longum subsp. longum reduced lung inflammation, inflammatory cytokine expression and adhesion factor expression and alleviated cigarette smoke-induced depletion in caecum butyrate. Thus, the probiotic administration of B. longum subsp. longum, irrespective of its acetate-producing capacity, alleviated cigarette smoke-induced inflammation and the depletion of cecal butyrate levels.
Anaerobaculum
Publisher: Wiley
Date: 10-09-2010
DOI: 10.1002/9781118960608.GBM01254
Abstract: An.ae.ro.ba'cu.lum. Gr. pref. an not Gr. n. aer air L. neut. n. baculum small stick N.L. neut. n. Anaerobaculum rod which grows in the absence of air. Synergistetes / Incertae Sedis / Incertae Sedis / Incertae Sedis / Anaerobaculum Straight to slightly curved rods. Occur singly or in pairs. Moderately thermophilic, chemorganotrophic anaerobes. May be motile by a single polar flagellum. In complex media, cells may or may not grow with sheathlike material that extends past the cell poles. Endospores have not been observed. Cells stain Gram‐negative. Ferment organic acids, protein extracts, and a limited range of carbohydrates. Sulfur, thiosulfate, and cystine are reduced to hydrogen sulfide. Sulfate, sulfite, and nitrate are not reduced. Isolated from production waters of a petroleum reservoir and an anaerobic lagoon treating wool‐scouring wastewater. DNA G + C content ( mol %): 44–51.5. Type species : Anaerobaculum thermoterrenum Rees, Patel, Grassia and Sheehy 1997, 153 VP .
Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds
Publisher: Proceedings of the National Academy of Sciences
Date: 20-07-2021
Abstract: Termites are textbook ex les of the “extended phenotype” given their ability to construct complex mounds and regulate environments. Here, we show that termites also control microbial composition and biogeochemical cycling in their mounds through their emissions of hydrogen. These emissions drive remarkable enrichments of mound bacteria that use hydrogen to drive aerobic respiration and sometimes carbon fixation (i.e., lithoautotrophs). Such mound communities efficiently consume all termite-produced hydrogen and even mediate atmospheric uptake, while termite-produced methane escapes to the atmosphere. This provides further evidence that hydrogen is a major substrate for aerobic bacteria and that the terrestrial hydrogen sink is highly responsive to elevated emissions.
Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C
Publisher: American Society for Microbiology
Date: 05-2014
Abstract: Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal disease around the globe, causing an estimated 380,000 deaths annually. The disease is caused by a wide variety of strains. Here, we report the genome sequence of ETEC strain B2C, which was isolated from an American soldier in Vietnam.
Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging
Publisher: American Society for Microbiology
Date: 31-12-2012
Abstract: Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus ( Cyanobacteria ) and the fast-growing, heterotrophic genus Pseudoalteromonas ( Gammaproteobacteria ). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas . Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus ), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth. IMPORTANCE Viral study suffers from an inability to link viruses to hosts en masse , and yet delineating “who infects whom” is fundamental to viral ecology and predictive modeling. This article describes viral tagging—a high-throughput method to investigate virus-host interactions by combining the fluorescent labeling of viruses for “tagging” host cells that can be analyzed and sorted using flow cytometry. Two cultivated hosts (the cyanobacterium Synechococcus and the gammaproteobacterium Pseudoalteromonas ) and their viruses (podo-, myo-, and siphoviruses) were investigated to validate the method. These lab-based experiments indicate that for most virus-host pairings, VT (viral tagging) adsorption is equivalent to traditional infection by liquid and plaque assays, with the exceptions being confined to promiscuous adsorption by Pseudoalteromonas siphoviruses. These experiments also reveal variability in life strategies across these oceanic virus-host systems with respect to infection conditions and host growth status, which highlights the need for further model system characterization to break open this virus-host interaction “black box.”
Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
Publisher: Springer Science and Business Media LLC
Date: 30-03-2010
Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome
Publisher: Springer Science and Business Media LLC
Date: 08-04-2200
Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans
Publisher: Springer Science and Business Media LLC
Date: 17-08-2023
DOI: 10.1186/S13104-023-06447-3
Abstract: In order to provide a better insight into the functional capacity of the human gut microbiome, we isolated a novel bacterium, “ Candidatus Intestinicoccus colisanans” gen. nov. sp. nov., and performed whole genome sequencing. This study will provide new insights into the functional potential of this bacterium and its role in modulating host health and well-being. We expect that this data resource will be useful in providing additional insight into the ersity and functional potential of the human microbiome. Here, we report the first draft genome sequences of “ Candidatus Intestinicoccus colisanans” strains MH27-1 and MH27-2, recovered from faeces collected from healthy human donors. The genomes were sequenced using short-read Illumina technology and whole-genome-based comparisons and phylogenomics reconstruction indicate that “ Candidatus Intestinicoccus colisanans” represents a novel genus and species within the family Acutalibacteraceae. Both genomes were estimated to be 98% completed and to range in size from 2.9 to 3.3 Mb with a G + C content of approximately 51%. The gene repertoire of “ Candidatus Intestinicoccus colisanans” indicate it is likely a saccharolytic gut bacterium.
Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations
Publisher: American Society for Microbiology
Date: 05-2014
Abstract: Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 in iduals by using culture-independent licon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typed Escherichia -dominated UTIs using licon pyrosequencing of the fimbrial adhesin gene, fimH . There were nine highly abundant fimH types, and each UTI s le was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eight E. coli urine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicated E. coli -mediated UTIs, single cultured isolates are diagnostic of the infection. IMPORTANCE In clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain ersity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods. Escherichia coli was the most common organism identified, and analysis of E. coli dominant UTI s les and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain ersity during UTI pathogenesis.
Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma
Publisher: European Respiratory Society (ERS)
Date: 02-12-2016
DOI: 10.1183/13993003.00405-2015
Abstract: Asthma is a chronic inflammatory disorder of the airways where bacteria may act as protagonists of chronic inflammation. Little is known about the relation of airway inflammation to the presence of specific bacterial taxa. We sought to describe the sputum microbiome in adults with poorly controlled asthma. DNA was extracted from induced sputum and microbial communities were profiled using 16S rRNA pyrosequencing. Bacterial species were characterised, and the relationship between microbial populations, asthma inflammatory subtypes and other covariates was explored. Real-time PCR was used to identify Tropheryma whipplei and Haemophilus influenzae in sputum. Adults with neutrophilic asthma had reduced bacterial ersity and species richness. Tropheryma was identified and confirmed with real-time PCR in 12 (40%) participants. Haemophilus occurred most often in a group of younger atopic males with an increased proportion of neutrophils. PCR confirmed the presence of H. influenzae in 35 (76%) participants with poorly controlled asthma. There are phenotype-specific alterations to the airway microbiome in asthma. Reduced bacterial ersity combined with a high prevalence of H. influenzae was observed in neutrophilic asthma, whereas eosinophilic asthma had abundant T. whipplei .
Correlative TEM/FISH Imaging of Microbial Communities
Publisher: Elsevier BV
Date: 2010
Prokaryotic taxonomy and nomenclature in the age of big sequence data
Publisher: Springer Science and Business Media LLC
Date: 06-04-2021
DOI: 10.1038/S41396-021-00941-X
Abstract: The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
A genome and gene catalog of glacier microbiomes
Publisher: Springer Science and Business Media LLC
Date: 27-06-2019
DOI: 10.1038/S41587-022-01367-2
Abstract: Glaciers represent a unique inventory of microbial genetic ersity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional ersity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Publisher: American Society for Microbiology
Date: 07-2006
DOI: 10.1128/AEM.03006-05
Abstract: A 16S rRNA gene database ( greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .
SNP-VISTA: An interactive SNP visualization tool
Publisher: Springer Science and Business Media LLC
Date: 12-0007
Abstract: Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in in iduals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental s les enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at ista/snpvista [1]. We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure 2) classification of SNPs, based on their location in the gene, frequency of occurrence in s les and allele composition 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences 4) integration of protein evolutionary conservation visualization and 5) display of automatically calculated recombination points that are user-editable. The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user.
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
Publisher: Springer Science and Business Media LLC
Date: 13-07-2014
DOI: 10.1038/NATURE13459
Abstract: Microbes and their viruses drive myriad processes across ecosystems ranging from oceans and soils to bioreactors and humans. Despite this importance, microbial ersity is only now being mapped at scales relevant to nature, while the viral ersity associated with any particular host remains little researched. Here we quantify host-associated viral ersity using viral-tagged metagenomics, which links viruses to specific host cells for high-throughput screening and sequencing. In a single experiment, we screened 10(7) Pacific Ocean viruses against a single strain of Synechococcus and found that naturally occurring cyanophage genome sequence space is statistically clustered into discrete populations. These population-based, host-linked viral ecological data suggest that, for this single host and seawater s le alone, there are at least 26 double-stranded DNA viral populations with estimated relative abundances ranging from 0.06 to 18.2%. These populations include previously cultivated cyanophage and new viral types missed by decades of isolate-based studies. Nucleotide identities of homologous genes mostly varied by less than 1% within populations, even in hypervariable genome regions, and by 42-71% between populations, which provides benchmarks for viral metagenomics and genome-based viral species definitions. Together these findings showcase a new approach to viral ecology that quantitatively links objectively defined environmental viral populations, and their genomes, to their hosts.
Metagenomics
Publisher: Springer Science and Business Media LLC
Date: 09-2008
DOI: 10.1038/455481A
The koala gut microbiome is largely unaffected by host translocation but rather influences host diet
Publisher: Frontiers Media SA
Date: 02-03-2023
DOI: 10.3389/FMICB.2023.1085090
Abstract: Translocation is a valuable and increasingly used strategy for the management of both threatened and overabundant wildlife populations. However, in some instances the translocated animals fail to thrive. Differences in diet between the source and destination areas may contribute to poor translocation outcomes, which could conceivably be exacerbated if the animals’ microbiomes are unsuited to the new diet and cannot adapt. In this study we tracked how the faecal microbiome of a specialist Eucalyptus folivore, the koala ( Phascolarctos cinereus ), changed over the course of a year after translocation. We assessed microbiome composition by 16S rRNA licon sequencing of faecal pellets. We found no significant overall changes in the faecal microbiomes of koalas post-translocation ( n = 17) in terms of microbial richness, ersity or composition when compared to the faecal microbiomes of koalas from an untranslocated control group ( n = 12). This was despite the translocated koalas feeding on a greater variety of Eucalyptus species after translocation. Furthermore, while differences between koalas accounted for half of the microbiome variation, estimated diets at the time of s ling only accounted for 5% of the variation in the koala microbiomes between s ling periods. By contrast, we observed that the composition of koala faecal microbiomes at the time of translocation accounted for 37% of between koala variation in post-translocation diet. We also observed that translocated koalas lost body condition during the first month post-translocation and that the composition of the koalas’ initial microbiomes were associated with the magnitude of that change. These findings suggest that the koala gut microbiome was largely unaffected by dietary change and support previous findings suggesting that the koala gut microbiome influences the tree species chosen for feeding. They further indicate that future research is needed to establish whether the koalas’ gut microbiomes are directly influencing their health and condition or whether aspects of the koala gut microbiomes are an indicator of underlying physiological differences or pathologies. Our study provides insights into how animal microbiomes may not always be affected by the extreme upheaval of translocation and highlights that responses may be host species-specific. We also provide recommendations to improve the success of koala translocations in the future.
The DMSO Reductase Family of Microbial Molybdenum Enzymes; Molecular Properties and Role in the Dissimilatory Reduction of Toxic Elements
Publisher: Informa UK Limited
Date: 2002
Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation
Publisher: American Society for Microbiology
Date: 03-2000
DOI: 10.1128/AEM.66.3.1175-1182.2000
Abstract: Laboratory-scale sequencing batch reactors (SBRs) as models for activated sludge processes were used to study enhanced biological phosphorus removal (EBPR) from wastewater. Enrichment for polyphosphate-accumulating organisms (PAOs) was achieved essentially by increasing the phosphorus concentration in the influent to the SBRs. Fluorescence in situ hybridization (FISH) using domain-, ision-, and sub ision-level probes was used to assess the proportions of microorganisms in the sludges. The A sludge, a high-performance P-removing sludge containing 15.1% P in the biomass, was comprised of large clusters of polyphosphate-containing coccobacilli. By FISH, % of the A sludge bacteria were β-2 Proteobacteria arranged in clusters of coccobacilli, strongly suggesting that this group contains a PAO responsible for EBPR. The second dominant group in the A sludge was the Actinobacteria . Clone libraries of PCR- lified bacterial 16S rRNA genes from three high-performance P-removing sludges were prepared, and clones belonging to the β-2 Proteobacteria were fully sequenced. A distinctive group of clones (sharing ≥98% sequence identity) related to Rhodocyclus spp. (94 to 97% identity) and Propionibacter pelophilus (95 to 96% identity) was identified as the most likely candidate PAOs. Three probes specific for the highly related candidate PAO group were designed from the sequence data. All three probes specifically bound to the morphologically distinctive clusters of PAOs in the A sludge, exactly coinciding with the β-2 Proteobacteria probe. Sequential FISH and polyphosphate staining of EBPR sludges clearly demonstrated that PAO probe-binding cells contained polyphosphate. Subsequent PAO probe analyses of a number of sludges with various P removal capacities indicated a strong positive correlation between P removal from the wastewater as determined by sludge P content and number of PAO probe-binding cells. We conclude therefore that an important group of PAOs in EBPR sludges are bacteria closely related to Rhodocyclus and Propionibacter .
An Expanded Genomic Representation of the Phylum Cyanobacteria
Publisher: Oxford University Press (OUP)
Date: 05-2014
DOI: 10.1093/GBE/EVU073
New foam-forming nocardioforms found in activated sludge
Publisher: IWA Publishing
Date: 1998
Dielectrophoresis-Based Discrimination of Bacteria at the Strain Level Based on Their Surface Properties
Publisher: Public Library of Science (PLoS)
Date: 16-10-2013
Environmental shotgun sequencing
Publisher: Wiley
Date: 15-04-2005
DOI: 10.1002/047001153X.G205313
Abstract: Shotgun sequencing of microbial communities is a promising means for delving into community function and interactions, population structure and dynamics, and bypassing the cultivation bottleneck in microbiology. However, this approach is mostly blind to low‐abundance species as it effectively s les only the dominant populations in a community. It also faces a number of technical challenges such as the assembly and separation of in idual genomes from a mixture of genomic fragments compounded by s ling unevenness and data scalability. Despite these limitations, environmental shotgun sequencing should rapidly advance the fields of microbial ecology and evolution.
Evolution of the Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and Other Pathogenic Streptococci
Publisher: Springer Science and Business Media LLC
Date: 10-2028
DOI: 10.1007/S00239-008-9117-1
Abstract: Hyaluronic acid (HA) is a ubiquitous linear polysaccharide in vertebrates and also is the capsule material of some pathogenic bacteria including group A and C streptococci. In bacteria, the HA synthase occurs in an operon (has) coding for enzymes involved in the production of HA precursors. We report two new members of the has operon family from Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) and Streptococcus equi subsp. equi (S. equi). The has operon of S. zooepidemicus contains, in order, hasA, hasB, hasC, glum, and pgi, whereas these genes are separated on two operons in S. equi (hasA, hasB, hasC and hasC, glmU, pgi). The transcription start site and a sigma(70) promoter were experimentally identified 50 bp upstream of hasA in S. zooepidemicus. We performed a phylogenetic analysis of each of the has operon genes to determine the evolutionary origin(s) of the streptococcal has operon. In contrast to other capsular and exopolysaccharide operons, has operons have undergone no detectable interspecies lateral gene transfers in their construction, instead relying on intragenome gene duplication for their assembly. Specifically, hasC and glmU appear to have been duplicated into the S. zooepidemicus has operon from remotely located but near-identical paralogues most likely to improve HA productivity by gene dosage in this streptococcus. The intragene rearrangements appear to be ongoing events and the two has operons of the S. equi subspecies represent two alternatives of the same gene arrangement. A scenario for the evolution of streptococcal has operons is proposed.
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations
Publisher: Springer Science and Business Media LLC
Date: 22-03-2021
Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Publisher: Frontiers Media SA
Date: 25-02-2016
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Publisher: Springer Science and Business Media LLC
Date: 11-09-2017
DOI: 10.1038/S41564-017-0012-7
Abstract: Challenges in cultivating microorganisms have limited the phylogenetic ersity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from ,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic ersity of bacterial and archaeal genome trees by % and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative ersity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
Publisher: Wiley
Date: 29-12-2009
DOI: 10.1111/J.1462-2920.2009.02051.X
Abstract: Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate ersity estimates. Although the per-base error of 16S rDNA licon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on ersity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA ersity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial ersity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere.
Fast, accurate error-correction of amplicon pyrosequences using Acacia
Publisher: Springer Science and Business Media LLC
Date: 27-04-2012
DOI: 10.1038/NMETH.1990
From deep sequencing to viral tagging: Recent advances in viral metagenomics
Publisher: Wiley
Date: 03-2013
Abstract: Culture-independent high-throughput sequencing has provided unprecedented insights into microbial ecology, particularly for Earth's most ubiquitous and erse inhabitants - the viruses. A plethora of methods now exist for lifying the vanishingly small amounts of nucleic acids in natural viral communities in order to sequence them, and sequencing depth is now so great that viral genomes can be detected and assembled even amid large concentrations of non-viral DNA. Complementing these advances in lification and sequencing is the ability to physically link fluorescently labeled viruses to their host cells via high-throughput flow sorting. Sequencing of such isolated virus-host pairs facilitates cultivation-independent exploration of the natural host range of viruses. Within the next decade, as these technologies become widespread, we can expect to see a systematic expansion of our knowledge of viruses and their hosts.
Metagenomics and Community Profiling: Culture-Independent Techniques in the Clinical Laboratory
Publisher: Elsevier BV
Date: 2013
Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils
Publisher: Wiley
Date: 03-06-2021
Abstract: Candidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome‐assembled genomes ( MAGs ), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order‐level clades within Ca . Dormibacterota. Metabolic reconstructions of these MAGs revealed the potential for aerobic metabolism, and versatile adaptations enabling persistence in the ‘extreme’ Antarctic environment. Primary amongst these adaptations were abilities to scavenge atmospheric H 2 and CO as energy sources, as well as using the energy derived from H 2 oxidation to fix atmospheric CO 2 via the Calvin–Bassham–Benson cycle, using a RuBisCO type IE . We propose that these allow Ca . Dormibacterota to persist using H 2 oxidation and grow using atmospheric chemosynthesis in terrestrial Antarctica. Fluorescence in situ hybridization revealed Ca . Dormibacterota to be coccoid cells, 0.3–1.4 μm in diameter, with some cells exhibiting the potential for a symbiotic or syntrophic lifestyle.
Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes
Publisher: American Society for Microbiology
Date: 15-10-2001
DOI: 10.1128/JB.183.20.6028-6035.2001
Abstract: A large fragment of the dissimilatory sulfite reductase genes ( dsrAB ) was PCR lified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For ex le, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive ision) and two members of the genus Thermodesulfobacterium (a separate bacterial ision) were monophyletic with δ-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that dsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the δ- Proteobacteria were laterally transferred across isions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for a dsrAB lateral gene transfer event also was found within the δ- Proteobacteria, affecting Desulfobacula toluolica . The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes in Archaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular ersity studies, they establish a framework to resolve the origins and ersification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.
Identifying microbial diversity in the natural environment: A molecular phylogenetic approach
Publisher: Elsevier BV
Date: 06-2011
DOI: 10.1016/0167-7799(96)10025-1
Abstract: Our knowledge of microbial bio ersity has been severely limited by relying on microorganisms that have been cultured these represent only a tiny fraction of the microbial ersity in the environment. Recently, however, recombinant DNA and molecular phylogenetic techniques have provided methods for characterizing natural microbial communities without the need to cultivate organisms. These techniques have allowed a glimpse of the complexity of microbial communities and the huge, largely untapped, biotechnological resource that they represent.
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
Publisher: Springer Science and Business Media LLC
Date: 19-09-2010
DOI: 10.1038/NMETH.1507
Abstract: The predominance of rRNAs in the transcriptome is a major technical challenge in sequence-based analysis of cDNAs from microbial isolates and communities. Several approaches have been applied to deplete rRNAs from (meta)transcriptomes, but no systematic investigation of potential biases introduced by any of these approaches has been reported. Here we validated the effectiveness and fidelity of the two most commonly used approaches, subtractive hybridization and exonuclease digestion, as well as combinations of these treatments, on two synthetic five-microorganism metatranscriptomes using massively parallel sequencing. We found that the effectiveness of rRNA removal was a function of community composition and RNA integrity for these treatments. Subtractive hybridization alone introduced the least bias in relative transcript abundance, whereas exonuclease and in particular combined treatments greatly compromised mRNA abundance fidelity. Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs.
Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples
Publisher: American Chemical Society (ACS)
Date: 13-06-2023
Chthoniobacter flavus gen. nov., sp. nov., the First Pure-Culture Representative of Subdivision Two, Spartobacteria classis nov., of the Phylum
Publisher: American Society for Microbiology
Date: 10-2004
DOI: 10.1128/AEM.70.10.5875-5881.2004
Abstract: The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six sub isions of the Verrucomicrobia are resolved by comparative analysis of 16S rRNA genes, mostly obtained directly from environmental s les. To date, only two of these sub isions (1 and 4) have characterized pure-culture representatives. We have isolated and characterized the first known pure-culture representative of sub ision 2. Strain Ellin428 is an aerobic heterotrophic bacterium that is able to grow with many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate. Cells are yellow, rod-shaped, nonmotile, and gram-stain negative, and they contain peptidoglycan with direct cross-linkages of the A1γ meso -Dpm type. The isolate grows well at 25°C on a variety of standard biological media, including some used in the routine cultivation of bacteria from soil. The pH range for growth is 4.0 to 7.0. Low levels of menaquinones MK-10 and MK-11 were detected. The major cellular fatty acids are C 14:0 , a-C 15:0 , C 16:1ω7c , and/or 2OH i-C 15:0 , and C 16:0 . The G+C content of the genomic DNA is 61 mol%. We propose a new genus and species, Chthoniobacter flavus gen. nov., sp. nov., with isolate Ellin428 as the type strain, and a new class for the sub ision to which it belongs, Spartobacteria classis nov. Environmental sequences indicate that the class Spartobacteria is largely represented by globally distributed, abundant, and active soil bacteria.
Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development
Publisher: Wiley
Date: 09-12-2021
Abstract: The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala ( Phascolarctos cinereus ). Joey koalas are thought to be inoculated with microorganisms by feeding on specialized maternal faeces (pap). We found that compared to faeces, pap has higher microbial density, higher microbial evenness and a higher proportion of rare taxa, which may facilitate the establishment of those taxa in joey koalas. We show that the microbiomes of captive joey koalas were on average more similar to those of their mothers than to other koalas, indicating strong maternal inheritance of the faecal microbiome, which can lead to intergenerational gut dysbiosis when the mother is ill. Directly after pap feeding, the joey koalas' microbiomes were enriched for milk‐associated bacteria including Bacteroides fragilis , suggesting a conserved role for this species across mammalian taxa. The joeys' microbiomes then changed slowly over 5 months to resemble those of adults by 1 year of age. The relative abundance of fibrolytic bacteria and genes involved in the degradation of plant cell walls also increased in the infants over this time, likely in response to an increased proportion of Eucalyptus leaves in their diets.
Increasing focus on environmental biotechnology in the face of pressing environmental challenges
Publisher: Elsevier BV
Date: 06-2007
A unified catalog of 204,938 reference genomes from the human gut microbiome
Publisher: Springer Science and Business Media LLC
Date: 20-09-2016
DOI: 10.1038/S41587-020-0603-3
Abstract: Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to in idual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.
Bioenergy feedstock‐specific enrichment of microbial populations during high‐solids thermophilic deconstruction
Publisher: Wiley
Date: 02-05-2011
DOI: 10.1002/BIT.23176
Abstract: Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched s les indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Publisher: Oxford University Press (OUP)
Date: 28-11-2015
COVID-19 pandemic reveals the peril of ignoring metadata standards
Publisher: Springer Science and Business Media LLC
Date: 19-06-2020
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys
Publisher: Springer Science and Business Media LLC
Date: 30-06-2011
A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Publisher: Frontiers Media SA
Date: 07-01-2016
Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance
Publisher: Frontiers Media SA
Date: 20-06-2023
DOI: 10.3389/FCHEM.2023.1196073
Abstract: β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn 2+ ) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical s les. B3-type MBLs display greater ersity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.
MICROTHRIX PARVICELLA IS A NOVEL, DEEP BRANCHING MEMBER OF THE ACTINOMYCETES SUBPHYLUM
Publisher: Elsevier BV
Date: 02-1995
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Publisher: Springer Science and Business Media LLC
Date: 28-07-2013
DOI: 10.1038/NATURE12375
Abstract: Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron, manganese and sulphate reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus 'Methylomirabilis oxyfera' can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of 'M. oxyfera' and a novel ANME lineage, ANME-2d. However, as 'M. oxyfera' can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and (13)C- and (15)N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting 'M. oxyfera' in the system. We propose the name Candidatus 'Methanoperedens nitroreducens' for the ANME-2d population and the family Candidatus 'Methanoperedenaceae' for the ANME-2d lineage. We predict that 'M. nitroreducens' and other members of the 'Methanoperedenaceae' have an important role in linking the global carbon and nitrogen cycles in anoxic environments.
Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges
Publisher: Springer Science and Business Media LLC
Date: 31-05-2007
Abstract: A fatal bulking phenomenon was found to occur occasionally in the methanogenic granular sludge of a mesophilic (35-40 degrees C), full-scale upflow anaerobic sludge blanket (UASB) reactor treating organic wastewater discharged from a sugar manufacturing factory. A vast number of filamentous cells were observed in the bulking sludge that were morphologically distinct from the previously recognized anaerobic bulking agent Anaerolinea thermophila. 16S rRNA gene-based analyses of the microbial populations in the bulking sludge revealed that the dominant filamentous organisms were members of proposed candidate bacterial phylum, KSB3. Fluorescence in situ hybridization (FISH) analysis of the healthy sludge granules showed that the KSB3 filaments were the dominant granule surface population suggesting that they are fundamental constituents of the sludge granules and that they occasionally overgrow in the reactor, possibly triggering the filamentous bulking. We surveyed 10 additional mesophilic and thermophilic anaerobic sludges for the presence and ersity of KSB3 populations. Bacteria closely related to the characterized KSB3 filaments were present in two types of mesophilically grown UASB sludge granules treating actual wastewater discharged from sugar-processing industries.
Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients
Publisher: PeerJ
Date: 15-09-2015
DOI: 10.7717/PEERJ.1223
Design and Evaluation of 16S rRNA-Targeted Oligonucleotide Probes for Fluorescence In Situ Hybridization
Publisher: Humana Press
Date: 2018
The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities
Publisher: IWA Publishing
Date: 02-1998
Abstract: Clone libraries were prepared from polymerase chain reaction lified 16S rDNAs from activated sludge community DNAs. Eight different libraries from a range of s les were prepared. From each library, up to 100 clones were examined. In some libraries, the clone inserts were grouped into operational taxonomic units (OTUs) by restriction enzyme analysis (REA). Then, either the clones or representatives of OTUs were partially sequenced using either 27f or 530f conserved bacterial primers. The sequence data was phylogenetically analysed to group the clones and the method currently gives the best insight into the activated sludge microbial community bio ersity. The method for clone library production is described and the pros and cons of the procedure are outlined. In summary, the use of clone libraries has resulted in the discovery of unimagined bio ersity in activated sludge. The abundance of some unpredicted bacterial groups (e.g. beta subclass Proteobacteria) and the paucity of expected ones (e.g. Acinetobacter) highlights the inadequacy of traditional culture dependent methods that rely on s le dilution and spread plate inoculation.
Metabolic flexibility allows generalist bacteria to become dominant in a frequently disturbed ecosystem
Publisher: Cold Spring Harbor Laboratory
Date: 13-02-2020
DOI: 10.1101/2020.02.12.945220
Abstract: Ecological theory suggests that habitat disturbance differentially influences distributions of generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and other conditions. Microbial community composition and function was profiled in intertidal and subtidal sediments using 16S licon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Microbial abundance and composition significantly differed with sediment depth and, to a lesser extent, s ling date. Several generalist taxa were highly abundant and prevalent in all s les, including within orders Woeseiales and Flavobacteriales genome reconstructions indicate these facultatively anaerobic taxa are highly metabolically flexible and adapt to fluctuations in resource availability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers (Desulfobacterales, Desulfobulbales) and proposed candidate phylum MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments whereas the generalist-associated processes of sulfide oxidation and hydrogenogenic fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. In addition, a manipulative experiment confirmed generalists outcompete specialist taxa during simulated habitat disturbance. Altogether, these findings suggest that metabolically flexible taxa become dominant in these highly dynamic environments, whereas metabolic specialism restricts bacteria to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
The characterization and description of representatives of 'G' bacteria from activated sludge plants
Publisher: Oxford University Press (OUP)
Date: 07-1997
DOI: 10.1046/J.1472-765X.1997.00176.X
Abstract: The name Tetracoccus cechii is proposed for two strains of the tetrad arranged cocci, previously known as 'G' bacteria, which were isolated from laboratory scale activated sludge plants in the Czech Republic and in Italy. They were morphologically, phenotypically and phylogenetically characterized and found to comprise a novel lineage in the alpha-3 group of the proteobacterial phylum in the domain Bacteria. The strains are Gram-negative and produce intracellular inclusions of poly-beta-hydroxybutyrate. Although commonly seen in activated sludge mixed liquor as cocci 1-2 microns in diameter, arranged in tetrads, in pure culture they can also grow in amorphous aggregations and the cells are generally more variable in their size and shape with coccobacilli as well as cocci being present. They are not able to grow phototrophically, nor can they reduce nitrate beyond nitrite nor grow anaerobically. The closest phylogenetic neighbours of T. cechii are Rhodobacter sphaeroides and R. capsulatus which are 93% similar by 16S rDNA comparison. Tetracoccus cechii is oxidase- and catalase-positive, non-motile and has an optimal growth temperature between 25 degrees and 35 degrees C. The 16S rRNA of T. cechii has a 21 nucleotide deletion in the V9 region (Escherichia coli positions 1258-1278) and this feature is a unique molecular synapomorphy in the alpha-3 group.
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Publisher: Springer Science and Business Media LLC
Date: 27-08-2018
DOI: 10.1038/NBT.4229
Abstract: Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary ergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the sub ision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales -Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes
Publisher: American Society for Microbiology
Date: 09-2003
DOI: 10.1128/AEM.69.9.5512-5518.2003
Abstract: During a molecular phylogenetic survey of extremely acidic (pH 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria . The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba . Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage s les, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage s les contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name “ Candidatus Captivus acidiprotistae.” To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.
Non-Sulfate-Reducing, Syntrophic Bacteria Affiliated with Desulfotomaculum Cluster I Are Widely Distributed in Methanogenic Environments
Publisher: American Society for Microbiology
Date: 03-2006
DOI: 10.1128/AEM.72.3.2080-2091.2006
Abstract: The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For ex le, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all s les examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB , which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.
Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers
Publisher: Oxford University Press (OUP)
Date: 07-2020
DOI: 10.1093/JTM/TAAA116
Abstract: Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool. Aircraft and cruise ship wastewater s les (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption–extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR licons from positive s les were sequenced to confirm assay specificity. SARS-CoV-2 RNA was detected in s les from both aircraft and cruise ship wastewater however concentrations were near the assay limit of detection. The analysis of multiple replicate s les and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR licons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods. The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, s ling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers.
Functional Characterization of Two New Variants in the Bone Morphogenetic Protein 7 Prodomain in Two Pairs of Monozygotic Twins With Hypospadias
Publisher: The Endocrine Society
Date: 22-02-2019
Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse
Publisher: Oxford University Press (OUP)
Date: 15-06-2020
Tracking seasonal changes in diversity of pollen allergen exposure: Targeted metabarcoding of a subtropical aerobiome
Publisher: Elsevier BV
Date: 12-2020
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments
Publisher: Springer Science and Business Media LLC
Date: 11-03-2019
DOI: 10.1038/S41564-019-0391-Z
Abstract: Permeable (sandy) sediments cover half of the continental margin and are major regulators of oceanic carbon cycling. The microbial communities within these highly dynamic sediments frequently shift between oxic and anoxic states, and hence are less stratified than those in cohesive (muddy) sediments. A major question is, therefore, how these communities maintain metabolism during oxic-anoxic transitions. Here, we show that molecular hydrogen (H
Genome-Based Microbial Taxonomy Coming of Age
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2016
GroopM: An automated tool for the recovery of population genomes from related metagenomes
Publisher: PeerJ
Date: 10-06-2014
DOI: 10.7287/PEERJ.PREPRINTS.409V1
Abstract: Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
Stimulation of aldrin and dieldrin loss from soils treated with carbon amendments and saturated-ring analogues
Publisher: Springer Science and Business Media LLC
Date: 08-1990
DOI: 10.1007/BF01700187
Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years
Publisher: Springer Science and Business Media LLC
Date: 06-10-2021
DOI: 10.1186/S40168-021-01151-5
Abstract: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically erse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) s les collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters. Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively. Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition.
Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MA19034
Abstract: Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new project GEBA VI extends these efforts to functional genomics, including pangenome and transcriptome sequencing and exometabolite analyses. As part of this project, investigators with interests in specific groups of prokaryotes are invited to submit s les for analysis at JGI.
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Publisher: Frontiers Media SA
Date: 24-04-2017
Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains
Publisher: Springer Science and Business Media LLC
Date: 17-05-2015
A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data
Publisher: Microbiology Society
Date: 03-2001
DOI: 10.1099/00207713-51-2-385
Abstract: The 16S rRNA gene (16S rDNA) is currently the most widely used gene for estimating the evolutionary history of prokaryotes. To date, there are more than 30,000 16S rDNA sequences available from the core databases, GenBank, EMBL and DDBJ. This great number may cause a dilemma when composing datasets for phylogenetic analysis, since the choice and number of reference organisms are known to affect the resulting tree topology. A group of sequences appearing monophyletic in one dataset may not be so in another. This can be especially problematic when establishing the relationships of distantly related sequences at the ision (phylum) level. In this study, a multiple-outgroup approach to resolving ision-level phylogenetic relationships is suggested using 16S rDNA data. The approach is illustrated by two case studies concerning the monophyly of two recently proposed bacterial isions, OP9 and OP10.
Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions
Publisher: Springer Science and Business Media LLC
Date: 26-06-2015
DOI: 10.1007/S00248-015-0641-4
Abstract: Synergistetes strain MFA1 is an asaccharolytic ruminal bacterium isolated based on its ability to degrade fluoroacetate, a plant toxin. The amino acid and peptide requirements of the bacterium were investigated under different culturing conditions. The growth of strain MFA1 and its fluoroacetate degradation rate were enhanced by peptide-rich protein hydrolysates (tryptone and yeast extract) compared to casamino acid, an amino acid-rich protein hydrolysate. Complete utilization and preference for arginine, asparagine, glutamate, glycine, and histidine as free amino acids from yeast extract were observed, while the utilization of serine, threonine, and lysine in free form and peptide-bound glutamate was stimulated during growth on fluoroacetate. A predominant peptide in yeast extract preferentially utilized by strain MFA1 was partially characterized by high-liquid performance chromatography-mass spectrometry as a hepta-glutamate oligopeptide. Similar utilization profiles of amino acids were observed between the co-culture of strain MFA1 with Methanobrevibacter smithii without fluoroacetate and pure strain MFA1 culture with fluoroacetate. This suggests that growth of strain MFA1 could be enhanced by a reduction of hydrogen partial pressure as a result of hydrogen removal by a methanogen or reduction of fluoroacetate.
Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models
Publisher: European Respiratory Society
Date: 04-09-2022
A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia
Publisher: Microbiology Society
Date: 09-06-2023
Abstract: Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia , according to the Genome Taxonomy Database. However, substantial additional ersity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales . Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.
CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea
Publisher: Springer Science and Business Media LLC
Date: 03-2008
DOI: 10.1038/NRMICRO1793
Abstract: Arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats that are separated by similarly sized non-repetitive spacers. CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism.
PHYLOGENETIC ANALYSIS AND TAXONOMIC HISTORY OF NOCARDIA-PINENSIS AND NOCARDIA-AMARAE
Publisher: Elsevier BV
Date: 02-1995
Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Publisher: Public Library of Science (PLoS)
Date: 16-11-2010
Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome
Publisher: American Society for Microbiology
Date: 05-2015
Abstract: Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity—the oral microbiome—by analyzing hundreds of s les obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012–2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE ( p 0.05 using the Mann-Whitney U-test). Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size
Publisher: Springer Science and Business Media LLC
Date: 08-2018
A call for standardized classification of metagenome projects
Publisher: Wiley
Date: 07-2010
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
Publisher: Springer Science and Business Media LLC
Date: 18-06-2007
In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery
Publisher: Elsevier
Date: 2013
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
Publisher: Springer Science and Business Media LLC
Date: 26-07-2012
Photosynthesis is not a universal feature of the phylum Cyanobacteria
Publisher: PeerJ
Date: 16-01-2014
DOI: 10.7287/PEERJ.PREPRINTS.204V1
Abstract: Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from human gut and groundwater s les. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six erse population genomes from gut and bioreactor s les supporting the inference that this lineage is non-photosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer, and refutes the long held belief that oxygenic photosynthesis is a universal feature of this phylum.
Photosynthesis is not a universal feature of the phylum Cyanobacteria
Publisher: PeerJ
Date: 17-03-2014
DOI: 10.7287/PEERJ.PREPRINTS.204V2
Abstract: Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from human gut and groundwater s les. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six erse population genomes from gut and bioreactor s les supporting the inference that this lineage is non-photosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer, and refutes the long held belief that oxygenic photosynthesis is a universal feature of this phylum.
The importance of designating type material for uncultured taxa
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.SYAPM.2018.07.003
Abstract: Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single lified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.
Insights into the phylogeny and coding potential of microbial dark matter
Publisher: Springer Science and Business Media LLC
Date: 14-07-2013
DOI: 10.1038/NATURE12352
Abstract: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional ersity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine erse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
Single Cell Whole Genome Amplification of Uncultivated Organisms
Publisher: Springer Berlin Heidelberg
Date: 2009
DOI: 10.1007/7171_2008_10
Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2021
DOI: 10.1101/2021.09.22.461432
Abstract: Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to ‘ E. flexneri’ ) because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli . Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli , present evidence supporting this reclassification, and show that assigning E. coli / Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.
Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community
Publisher: Microbiology Society
Date: 02-2003
Abstract: The reductive dechlorination (RD) of tetrachloroethene (PCE) to vinyl chloride (VC) and, to a lesser extent, to ethene (ETH) by an anaerobic microbial community has been investigated by studying the processes and kinetics of the main physiological components of the consortium. Molecular hydrogen, produced by methanol-utilizing acetogens, was the electron donor for the PCE RD to VC and ETH without forming any appreciable amount of other chlorinated intermediates and in the near absence of methanogenic activity. The microbial community structure of the consortium was investigated by preparing a 16S rDNA clone library and by fluorescence in situ hybridization (FISH). The PCR primers used in the clone library allowed the harvest of 16S rDNA from both bacterial and archaeal members in the community. A total of 616 clones were screened by RFLP analysis of the clone inserts followed by the sequencing of RFLP group representatives and phylogenetic analysis. The clone library contained sequences mostly from hitherto undescribed bacteria. No sequences similar to those of the known RD bacteria like 'Dehalococcoides ethenogenes' or Dehalobacter restrictus were found in the clone library, and none of these bacteria was present in the RD consortium according to FISH. Almost all clones fell into six previously described phyla of the bacterial domain, with the majority (56.6 %) being deep-branching members of the Spirochaetes phylum. Other clones were in the Firmicutes phylum (18.5 %), the Chloroflexi phylum (16.4 %), the Bacteroidetes phylum (6.3 %), the Synergistes genus (1.1 %) and a lineage that could not be affiliated with existing phyla (1.1 %). No archaeal clones were found in the clone library. Owing to the phylogenetic novelty of the microbial community with regard to previously cultured micro-organisms, no specific microbial component(s) could be hypothetically affiliated with the RD phenotype. The predominance of Spirochaetes in the microbial consortium, the main group revealed by clone library analysis, was confirmed by FISH using a purposely developed probe.
IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease.
Publisher: American Society of Hematology
Date: 05-05-2021
Abstract: Immunopathology and intestinal stem cell (ISC) loss in the gastrointestinal (GI) tract is the prima facie manifestation of graft-versus-host disease (GVHD) and is responsible for significant mortality after allogeneic bone marrow transplantation (BMT). Approaches to prevent GVHD to date focus on immune suppression. Here, we identify interferon-λ (IFN-λ interleukin-28 [IL-28]/IL-29) as a key protector of GI GVHD immunopathology, notably within the ISC compartment. Ifnlr1−/− mice displayed exaggerated GI GVHD and mortality independent of Paneth cells and alterations to the microbiome. Ifnlr1−/− intestinal organoid growth was significantly impaired, and targeted Ifnlr1 deficiency exhibited effects intrinsic to recipient Lgr5+ ISCs and natural killer cells. PEGylated recombinant IL-29 (PEG-rIL-29) treatment of naive mice enhanced Lgr5+ ISC numbers and organoid growth independent of both IL-22 and type I IFN and modulated proliferative and apoptosis gene sets in Lgr5+ ISCs. PEG-rIL-29 treatment improved survival, reduced GVHD severity, and enhanced epithelial proliferation and ISC-derived organoid growth after BMT. The preservation of ISC numbers in response to PEG-rIL-29 after BMT occurred both in the presence and absence of IFN-λ–signaling in recipient natural killer cells. IFN-λ is therefore an attractive and rapidly testable approach to prevent ISC loss and immunopathology during GVHD.
Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)
Publisher: Wiley
Date: 05-2006
DOI: 10.1111/J.1462-2920.2005.00973.X
Abstract: Native bacteria, Pseudomonas and filamentous bacteria were quantified and localized on wheat roots grown in the field using fluorescence in situ hybridization (FISH). Seminal roots were s led through the season from unploughed soil in a conservation farming system. Such soils are spatially heterogeneous, and many roots grow slowly through hard soil with cracks and pores containing dead roots remnant from previous crops. Root and rhizosphere morphology, and contact with soil particles were preserved, and autofluorescence was avoided by observing sections in the far-red with Cy5 and Cy5.5 fluorochromes. Spatial analyses showed that bacteria were embedded in a stable matrix (biofilm) within 11 microm of the root surface (range 2-30 microm) and were clustered on 40% of roots. Half the clusters co-located with axial grooves between epidermal cells, soil particles, cap cells or root hairs the other half were not associated with visible features. Across all wheat roots, although variable, bacteria averaged 15.4 x 10(5) cells per mm(3) rhizosphere, and of these, Pseudomonas and filaments comprised 10% and 4%, respectively, with minor effects of s le time, and no effect of plant age. Root caps were most heavily colonized by bacteria along roots, and elongation zones least heavily colonized. Pseudomonas varied little with root development and were 17% of bacteria on the elongation zone. Filamentous bacteria were not found on the elongation zone. The most significant factor to rhizosphere populations along a wheat root, however, was contact with dead root remnants, where Pseudomonas were reduced but filaments increased to 57% of bacteria (P < 0.001). This corresponded with analyses of root remnants showing they were heavily colonized by bacteria, with 48% filaments (P < 0.001) and 1.4%Pseudomonas (P = 0.014). Efforts to manage rhizosphere bacteria for sustainable agricultural systems should continue to focus on root cap and mucilage chemistry, and remnant roots as sources of beneficial bacteria.
Defining the core Arabidopsis thaliana root microbiome
Publisher: Springer Science and Business Media LLC
Date: 08-2012
DOI: 10.1038/NATURE11237
Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
Publisher: Public Library of Science (PLoS)
Date: 05-08-2014
The Enduring Legacy of Small Subunit rRNA in Microbiology
Publisher: Wiley
Date: 03-05-2011
Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice
Publisher: Informa UK Limited
Date: 13-01-2020
Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?
Publisher: Frontiers Media SA
Date: 02-02-2023
DOI: 10.3389/FONC.2023.1091379
Abstract: Cutaneous squamous cell carcinoma (cSCC) and its premalignant precursor, actinic keratosis (AK), present a global health burden that is continuously increasing despite extensive efforts to promote sun safety. Chronic UV exposure is a recognized risk factor for the development of AK and cSCC. However, increasing evidence suggests that AK and cSCC is also associated with skin microbiome dysbiosis and, in particular, an overabundance of the bacterium Staphylococcus aureus ( S. aureus). Studies have shown that S. aureus -derived toxins can contribute to DNA damage and lead to chronic upregulation of proinflammatory cytokines that may affect carcinogenesis. Eradication of S. aureus from AK lesions and restoration of a healthy microbiome may therefore represent a therapeutic opportunity to alter disease progression. Whilst antibiotics can reduce the S. aureus load, antibiotic resistant S. aureus pose an increasing global public health threat. The use of specific topically delivered probiotics has been used experimentally in other skin conditions to restore eubiosis, and could therefore also present a non-invasive treatment approach to decrease S. aureus colonization and restore a healthy skin microbiome on AK lesions. This article reviews mechanisms by which S. aureus may contribute to cutaneous carcinogenesis, and discusses hypotheses and theories that explore the therapeutic potential of specific bacterial species which compete with S. aureus in an attempt to restore microbial eubiosis in skin.
Comparative Metagenomics of Microbial Communities
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-04-2005
Abstract: The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the s led environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
Road Map of the PhylumC ampylobacterota
Publisher: Wiley
Date: 16-09-2019
DOI: 10.1002/9781118960608.BM00040
Abstract: The C ylobacterota is a novel phylum created from the reclassification of the proteobacterial class Epsilonproteobacteria and order Desulfurellales ( Deltaproteobacteria ). The phylum is organized according to phylogenies based on a concatenated alignment of 120 conserved protein marker sequences and the 16S rRNA gene. Like any phylogenetic inference, this road map is a hypothesis based on the data available at the time of writing and may be subject to change as new species are described, or other gene sequences considered. This road map incorporates relative evolutionary ergence to normalize subordinate ranks. It, therefore, includes a number of changes at the rank of order, family, and genus, which would otherwise not be affected by the merging of the former lineages.
Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Publisher: Springer Science and Business Media LLC
Date: 25-05-2018
DOI: 10.1038/S41598-018-26484-4
Abstract: The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic ersity, typically dominated by Escherichia fergusonii , and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the ersity-stability hypothesis in the context of bacterial ecosystems.
A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes
Publisher: American Society for Microbiology
Date: 07-11-2018
Abstract: Actinic keratosis (AK) and cutaneous squamous cell carcinoma (SCC) are two of the most common dermatologic conditions in Western countries and cause substantial morbidity worldwide. The role of human papillomaviruses under these conditions has been well studied yet remains inconclusive. One PCR-based study has investigated bacteria in the etiology of these conditions however, no study has investigated the microbiomes of AK and SCC more broadly. We longitudinally profiled the microbiomes of 112 AK lesions, profiled cross sections of 32 spontaneously arising SCC lesions, and compared these to matching nonlesional photodamaged control skin sites. We identified commonly occurring strains of Propionibacterium and Malassezia at higher relative abundances on nonlesional skin than in AK and SCC lesions, and strains of Staphylococcus aureus were relatively more abundant in lesional than nonlesional skin. These findings may aid in the prevention of SCC.
An ecological and phylogenetic investigation of a bacterial biofilm growing on the cooling coils in an air-handling system
Publisher: University of Queensland Library
Interferon Lambda Protects Gastrointestinal Stem Cells from Acute Gvhd
Publisher: Elsevier BV
Date: 03-2021
A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells
Publisher: Springer Science and Business Media LLC
Date: 04-09-2008
Abstract: Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 degrees C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37 mW m(-2) with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray and clone library analysis with small subunit ribosomal RNA (16S rRNA) and ribosomal RNA gene (16S rDNA). The results illustrated the dominance (80% of clone library sequences) of the Firmicutes in electricity production. Similarly, rRNA sequences from Firmicutes accounted for 50% of those taxa that increased in relative abundance from current-producing MFCs, implying their functional role in current production. We complemented these analyses by isolating the first organisms from a thermophilic MFC. One of the isolates, a Firmicutes Thermincola sp. strain JR, not only produced more current than known organisms (0.42 mA) in an H-cell system but also represented the first demonstration of direct anode reduction by a member of this phylum. Our research illustrates the importance of using a variety of molecular and culture-based methods to reliably characterize bacterial communities. Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation.
High-resolution phylogenetic microbial community profiling
Publisher: Springer Science and Business Media LLC
Date: 09-02-2016
2125. Staphylococcus Species Identification by Fourier Transform Infrared (FTIR) Spectroscopic Techniques: A Cross-Lab Study
Publisher: Oxford University Press (OUP)
Date: 10-2019
Abstract: Staphylococcus aureus is well known to be associated with atopic dermatitis. Recent studies also report S. aureus presence in lesional skin of squamous cell carcinoma (SCC) and its precursor lesion, actinic keratosis (AK). Therefore, it is of potential clinical interest to monitor skin S. aureus colonization on AK lesions. Fourier transform infrared (FTIR) spectroscopy is a cost-effective, nondestructive, and reagent-free technique for rapid microbial identification. It is based on the use of spectral databases developed with well-characterized strains in conjunction with the application of multivariate statistical analysis to elaborate classification models. In the present cross-lab study, spectral databases containing FTIR spectra of over 1000 staphylococcal isolates obtained from reference and clinical microbiology laboratories across Canada were employed in the FTIR spectroscopic identification of Staphylococcus spp. isolated from AK, SCC and perilesional skin of patients at the Princess Alexandra Hospital Dermatology Clinic in Brisbane, Australia. FTIR spectra of 51 staphylococcal isolates from AK, SCC and perilesional skin were acquired by both attenuated total reflectance (ATR)-FTIR and transflection-FTIR spectroscopy. All isolates had been previously characterized by 16S rRNA sequencing. ATR- and transflection-FTIR spectra were recorded in triplicate from isolated colonies taken from the same agar plate. Identification of the bacteria was based on the similarities of their spectra with those in ATR- and transflection-FTIR spectral databases originating from the Canadian lab. Among the 51 staphylococcal isolates included in this study, identification of S. aureus (n = 24) with 100% specificity and 100% sensitivity was achieved by both ATR- and transflection-FTIR spectroscopy. Overall, FTIR-based species identification was in 90.2% concordance with 16S rRNA sequencing. This cross-lab study demonstrates the applicability of Canadian isolate-based ATR- and transflection-FTIR spectral databases for the identification of clinical staphylococcal isolates obtained in Australia. The results support the potential utility of FTIR spectroscopic techniques to monitor skin S. aureus colonization on AK lesions. All authors: No reported disclosures.
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages
Publisher: Springer Science and Business Media LLC
Date: 28-06-2021
DOI: 10.1038/S43705-021-00032-0
Abstract: Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca . Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils
Publisher: Wiley
Date: 09-2022
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Publisher: Springer Science and Business Media LLC
Date: 20-05-2019
DOI: 10.1038/S41564-019-0448-Z
Abstract: Viruses of bacteria and archaea are important players in global carbon cycling as well as drivers of host evolution, yet the taxonomic classification of viruses remains a challenge due to their genetic ersity and absence of universally conserved genes. Traditional classification approaches employ a combination of phenotypic and genetic information which is no longer scalable in the era of bulk viral genome recovery through metagenomics. Here, we evaluate a phylogenetic approach for the classification of tailed double-stranded DNA viruses from the order Caudovirales by inferring a phylogeny from the concatenation of 77 single-copy protein markers using a maximum-likelihood method. Our approach is largely consistent with the International Committee on Taxonomy of Viruses, with 72 and 89% congruence at the subfamily and genus levels, respectively. Discrepancies could be attributed to misclassifications and a small number of highly mosaic genera confounding the phylogenetic signal. We also show that confidently resolved nodes in the concatenated protein tree are highly reproducible across different software and models, and conclude that the approach can serve as a framework for a rank-normalized taxonomy of most tailed double-stranded DNA viruses.
Wastewater monitoring for SARS-CoV-2
Publisher: CSIRO Publishing
Date: 2021
DOI: 10.1071/MA21006
Abstract: Wastewater monitoring (WM) of SARS-CoV-2 from sewers was applied throughout the world early in the COVID-19 pandemic. Sharing of protocols and experiences in WM of SARS-CoV-2 by national and international researchers and practitioners has been vital to ensuring the sensitivity and specificity of the methods. WM has been a valuable adjunct to human clinical testing, and when positive results occur in sewage, community testing has been increased. WM findings allow public health officials to track and respond to the impacts of loosening lockdown restrictions, demonstrating when return to normal social activities might occur without a resurgence of rapid community transmission, and they are particularly useful in areas with low human case numbers and/or low clinical testing rates. New research is required to address several practical knowledge gaps, for ex le, s ling protocols, prediction of case prevalence from viral numbers by modelling, and determination of detection limits. Communication to the Australian public of WM of SARS-CoV-2 has been via interactive, visual dashboards. Once SARS-CoV-2 vaccinations are introduced, WM could help track the underlying circulation of the virus in the population, the spread of known variants and its future evolution.
‘Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep‐branching clade of Deltaproteobacteria and a putative homoacetoge
Publisher: Wiley
Date: 21-04-2016
Abstract: Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence of a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH ) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.
Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated
Publisher: Springer Science and Business Media LLC
Date: 22-03-2023
DOI: 10.1186/S12915-023-01524-2
Abstract: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with ‘low-methane’ emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum , as well as Methanobrevibacter , Methanosphaera , and Methanomassiliicoccales . Despite sporadic reports of Methanocorpusculum from stool s les of various animal species, there remains little information on the impacts of these methanogens on their hosts. Here, we characterise novel host-associated species of Methanocorpusculum , to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat ( Vombatus ursinus ) and mahogany glider ( Petaurus gracilis ), along with the cultivation of one axenic isolate from each respective animal M. vombati (sp. nov.) and M. petauri (sp. nov.). Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum . These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.
Corrigendum: ‘A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia’
Publisher: Microbiology Society
Date: 09-08-2023
A Bioinformatician's Guide to Metagenomics
Publisher: American Society for Microbiology
Date: 12-2008
Abstract: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for s ling and data generation including s le and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
Publisher: Microbiology Society
Date: 11-2020
Abstract: The class Deltaproteobacteria comprises an ecologically and metabolically erse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio- like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia . Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria . Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria , and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota , which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal c cThe EMBL accession numbers for the sequences reported in this pap
Publisher: Microbiology Society
Date: 08-2002
DOI: 10.1099/00221287-148-8-2309
Abstract: Most filamentous bacteria in biological nutrient removal (BNR) processes have not been identified beyond their morphotype and simple staining reactions. Furthermore, the majority of sludge filaments observed under the microscope do not hybridize to commonly used phylogenetic probes for well characterized bacterial phyla such as the Proteobacteria, Actinobacteria, Firmicutes and BACTEROIDETES: Specific 16S rRNA-targeted oligonucleotide probes were designed for the phylum Chloroflexi (green non-sulfur bacteria) and optimized for use in fluorescence in situ hybridization. Chloroflexi have been implicated in BNR systems by phylogenetic identification of filamentous bacteria isolated by micromanipulation from sludge and culture-independent molecular phylogenetic surveys. The predominant morphotype responding to the probes was filamentous and these filaments were generally abundant in 10 Australian full-scale and two laboratory-scale BNR s les examined. Filamentous bacteria responding to a sub ision 1 Chloroflexi probe were rare in the s les, whereas sub ision 3 Chloroflexi filaments were very common in some sludges. This is in direct contrast to results obtained from molecular phylogenetic surveys of BNR systems where most sludge 16S rDNA clones belong to sub ision 1 and only a few to sub ision 3. It is suggested that filamentous bacteria belonging to the Chloroflexi phylum account for a large fraction of phylogenetically uncharacterized filaments in BNR systems and are likely to be abundant in such systems on a global scale.
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin
Publisher: Frontiers Media SA
Date: 25-01-2022
DOI: 10.3389/FMICB.2021.789042
Abstract: Squamous cell carcinoma (SCC) is a common type of skin cancer that typically arises from premalignant precursor lesions named actinic keratoses (AK). Chronic inflammation is a well-known promoter of skin cancer progression. AK and SCC have been associated with an overabundance of the bacterium Staphylococcus aureus ( S. aureus ). Certain secreted products from S. aureus are known to promote cutaneous pro-inflammatory responses however, not all S. aureus strains produce these. As inflammation plays a key role in SCC development, we investigated the pro-inflammatory potential and toxin secretion profiles of skin-cancer associated S. aureus . Sterile culture supernatants (“secretomes”) of S. aureus clinical strains isolated from AK and SCC were applied to human keratinocytes in vitro. Some S. aureus secretomes induced keratinocytes to overexpress inflammatory mediators that have been linked to skin carcinogenesis, including IL-6, IL-8, and TNFα. A large phenotypic variation between the tested clinical strains was observed. Strains that are highly pro-inflammatory in vitro also caused more pronounced skin inflammation in mice. Proteomic characterization of S. aureus secretomes using mass spectrometry established that specific S. aureus enzymes and cytolytic toxins, including hemolysins, phenol-soluble modulins, and serine proteases, as well as currently uncharacterized proteins, correlate with the pro-inflammatory S. aureus phenotype. This study is the first to describe the toxin secretion profiles of AK and SCC-associated S. aureus , and their potential to induce a pro-inflammatory environment in the skin. Further studies are needed to establish whether these S. aureus products promote SCC development by mediating chronic inflammation.
Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease
Publisher: Springer Science and Business Media LLC
Date: 18-11-2020
DOI: 10.1038/S41467-020-19701-0
Abstract: Chronic obstructive pulmonary disease (COPD) is the third commonest cause of death globally, and manifests as a progressive inflammatory lung disease with no curative treatment. The lung microbiome contributes to COPD progression, but the function of the gut microbiome remains unclear. Here we examine the faecal microbiome and metabolome of COPD patients and healthy controls, finding 146 bacterial species differing between the two groups. Several species, including Streptococcus sp000187445 , Streptococcus vestibularis and multiple members of the family Lachnospiraceae , also correlate with reduced lung function. Untargeted metabolomics identifies a COPD signature comprising 46% lipid, 20% xenobiotic and 20% amino acid related metabolites. Furthermore, we describe a disease-associated network connecting Streptococcus parasanguinis_B with COPD-associated metabolites, including N-acetylglutamate and its analogue N-carbamoylglutamate. While correlative, our results suggest that the faecal microbiome and metabolome of COPD patients are distinct from those of healthy in iduals, and may thus aid in the search for biomarkers for COPD.
The placental microbiome; microbial presence in nature’s transplant
Publisher: Elsevier BV
Date: 09-2015
Evaluating DNA extraction methods for community profiling of pig hindgut microbial community
Publisher: Public Library of Science (PLoS)
Date: 11-11-2015
A standardized archaeal taxonomy for the Genome Taxonomy Database
Publisher: Springer Science and Business Media LLC
Date: 21-06-2021
DOI: 10.1038/S41564-021-00918-8
Abstract: The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary ergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.
Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala
Publisher: Springer Science and Business Media LLC
Date: 21-08-2019
A new species of Burkholderia isolated from sugarcane roots promotes plant growth
Publisher: Wiley
Date: 19-12-2014
Potential use of a combined ozone and zeolite system for gaseous toluene elimination
Publisher: Elsevier BV
Date: 05-2007
DOI: 10.1016/J.JHAZMAT.2006.08.077
Abstract: This study investigated the performance of a combined ozone and zeolite system in eliminating gaseous toluene which is a major contaminant in many industrial and indoor environments. The hypothesis that the removal of toluene by ozone can be substantially affected by confining the oxidation reaction in a zeolite structure was evaluated. The degradation of toluene seemed to be contributed by the active oxygen atom generated from the decomposition of ozone at the Lewis acid sites in the zeolite 13X. Air containing toluene levels at 1.5, 2 and 3 ppm was injected with ozone in the range of 0-6 ppm before being vented into a fixed amount of 3600 g zeolite 13X with 90 mm bed-length. The experimental results showed that the elimination rate of toluene was significantly enhanced when compared to using zeolite or ozone alone. In particular, over 90% of the 1.5 ppm toluene was removed when 6 ppm ozone was used at 40% relative humidity level. Deactivation of the zeolite 13X after a few hours of reactions under the current experimental conditions was probably due to the adsorbed water, carbon dioxide and the reaction by-products. The residue species left in the zeolite and the intermediate species in the exhaust gas stream were characterized by FT-IR, GC-MS and HP-LC methods, respectively. A distinctive peak of O atom attached to the Lewis acid site at 1380 cm(-1) was found in the FT-IR spectrum and trace amount of aldehydes was found to be the reaction by-products.
A renaissance for the pioneering 16S rRNA gene
Publisher: Elsevier BV
Date: 10-2008
DOI: 10.1016/J.MIB.2008.09.011
Abstract: Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related s les (e.g. spatial and temporal series) and improved metadata, and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and erse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.
Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System
Publisher: Public Library of Science (PLoS)
Date: 18-05-2011
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal
Publisher: Wiley
Date: 10-09-2008
Characterization of the juvenile koala gut microbiome across wild populations
Publisher: Wiley
Date: 12-01-2022
Abstract: In this study we compared the faecal microbiomes of wild joey koalas ( Phascolarctos cinereus ) to those of adults, including their mothers, to establish whether gut microbiome maturation and inheritance in the wild is comparable to that seen in captivity. Our findings suggest that joey koala microbiomes slowly shift towards an adult assemblage between 6 and 12 months of age, as the microbiomes of 9‐month‐old joeys were more similar to those of adults than those of 7‐month‐olds, but still distinct. At the phylum level, differences between joeys and adults were broadly consistent with those in captivity, with Firmicutes increasing in relative abundance over the joeys' development and Proteobacteria decreasing. Of the fibre‐degrading genes that increased in abundance over the development of captive joeys, those involved in hemicellulose and cellulose degradation, but not pectin degradation, were also generally found in higher abundance in adult wild koalas compared to 7‐month‐olds. Greater maternal inheritance of the faecal microbiome was seen in wild than in captive koalas, presumably due to the more solitary nature of wild koalas. This strong maternal inheritance of the gut microbiome could contribute to the development of localized differences in microbiome composition, population health and diet through spatial clustering of relatives.
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
Publisher: American Society for Microbiology
Date: 15-01-1998
DOI: 10.1128/JB.180.2.366-376.1998
Abstract: A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal ersity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609–1613, 1994). Small-subunit rRNA genes (rDNA) were lified directly from OP sediment DNA by PCR with universally conserved or Bacteria -specific rDNA primers and cloned. Unique rDNA types among clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (≥98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial isions (main phyla kingdoms) 30% were unaffiliated with recognized bacterial isions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, ision level lineages termed candidate isions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium , or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing δ- Proteobacteria . The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of lified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial ersity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of ision level bacterial phylogenetic ersity is collated and summarized.
Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients
Publisher: Springer Science and Business Media LLC
Date: 02-2022
DOI: 10.1038/S43705-022-00095-7
Abstract: Actinic keratoses (AK) arise in severely photo-damaged skin and can progress to squamous cell carcinomas (SCC). AK and SCC are common in Caucasian populations, and immunosuppressed in iduals have a markedly higher risk of developing SCC. An overabundance of Staphylococcus aureus has been reported in AK and SCC lesions of immunocompetent in iduals, however, the AK/SCC microbiome in immunosuppressed cohorts has not been investigated. Here, the microbial profile and bacterial load of AK, SCC and control skin swabs from 32 immunosuppressed organ transplant recipients were characterised via SSU rRNA gene sequencing and qPCR, and compared to a previously described immunocompetent cohort. Although the taxonomic composition of skin swab s les was mostly subject-specific, significant differences were observed between control skin, AK, and SCC in both cohorts. Surface bacterial load was increased and alpha ersity decreased in AK and SCC compared to control skin due to an increased abundance of Staphylococcus species and relative decrease of skin commensals. Staphylococcus epidermidis predominated on SCC from transplant recipients in contrast to SCC of immunocompetent subjects dominated by S. aureus . In conclusion, AK and SCC of immunosuppressed and immunocompetent subjects present with distinctive microbial dysbioses, which may be relevant to SCC pathogenesis and progression.
Characterization of a highly efficient antibiotic-degrading metallo-beta-lactamase obtained from an uncultured member of a permafrost community
Publisher: Oxford University Press (OUP)
Date: 2017
DOI: 10.1039/C7MT00195A
Abstract: Microorganisms in the permafrost contain a potent mechanism to inactivate antibiotics.
Greengenes2 unifies microbial data in a single reference tree
Publisher: Springer Science and Business Media LLC
Date: 27-07-2023
DOI: 10.1038/S41587-023-01845-1
Abstract: Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR lification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same s les agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes
Publisher: Oxford University Press (OUP)
Date: 2023
Abstract: The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The ision of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
Publisher: Microbiology Society
Date: 2003
Abstract: A significant number of chimeric 16S rDNA sequences of erse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.
Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013
Publisher: Springer Science and Business Media LLC
Date: 30-07-2013
DOI: 10.4056/SIGS.4638348
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57
Publisher: Springer Science and Business Media LLC
Date: 06-09-2016
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
Publisher: Oxford University Press (OUP)
Date: 07-2006
DOI: 10.1093/NAR/GKL244
Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil
Publisher: Public Library of Science (PLoS)
Date: 29-04-2011
Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll a-Containing Bacteria and Description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., a
Publisher: Microbiology Society
Date: 07-1994
DOI: 10.1099/00207713-44-3-427
Abstract: We analyzed the 16S ribosomal DNAs of three obligately aerobic, bacteriochlorophyll a-containing bacteria, "Roseococcus thiosulfatophilus," "Erythromicrobium ramosum," and new isolate T4T (T = type strain), which was obtained from a marine cyanobacterial mat. "Roseococcus thiosulfatophilus" is a member of the alpha-1 subclass of the Proteobacteria and is moderately related to Rhodopila globiformis, Thiobacillus acidophilus, and Acidiphilium cryptum (level of sequence similarity, 90%). "Erythromicrobium ramosum" and isolate T4T are closely related to Erythrobacter longus and Porphyrobacter neustonensis (level of sequence similarity, 95%). These organisms are members of the alpha-4 subclass of the Proteobacteria. Strain T4T is a motile, red or orange bacterium. The major carotenoids are bacteriorubixanthinal and erythroxanthin sulfate. In vivo measurements revealed bacteriochlorophyll absorption maxima at 377, 590, 800, and 868 nm. Strain T4T grows in the presence of 5 to 96/1000 salinity and uses glucose, fructose, acetate, pyruvate, glutamate, succinate, and lactate as substrates. On the basis of its distinct phylogenetic position and phenotypic characteristics which are different from those of Erythrobacter longus, we propose that strain T4T should be placed in a new species of the genus Erythrobacter, Erythrobacter litoralis. The descriptions of "Roseococcus thiosulfatophilus" and "Erythromicrobium ramosum" are emended.
The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application
Publisher: Wiley
Date: 30-07-2016
Abstract: Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field-grown sugarcane with industry-standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root-enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root-associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
Publisher: Oxford University Press (OUP)
Date: 30-07-2101
DOI: 10.1093/NAR/GKP848
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Publisher: Springer Science and Business Media LLC
Date: 24-06-2021
DOI: 10.1038/S41564-021-00928-6
Abstract: Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of ersity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond
Publisher: Office of Scientific and Technical Information (OSTI)
Date: 06-2007
DOI: 10.2172/960403
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts
Publisher: Research Square Platform LLC
Date: 13-10-2021
DOI: 10.21203/RS.3.RS-948000/V1
Abstract: Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, hydrogen oxidising bacteria support primary production through a novel carbon fixation process reliant on the chemoautotrophy-associated RuBisCO form IE. Here, biochemical assays show that atmospheric chemosynthesis occurs globally for primary production, contributing significantly to autotrophic carbon fixation throughout arid to hyperarid deserts in Antarctica, the high Arctic, and the Tibetan Plateau. Taxonomic and functional analyses were performed on 230 dereplicated medium-to-high quality metagenome-assembled genomes (MAGs) derived from 18 cold desert metagenomes and an additional 24,080 publicly available genomes. We infer that atmospheric chemosynthetic bacteria are widespread across environmental and clinical s les, increasing our knowledge of the bacterial phyla genetically capable of atmospheric chemosynthesis to seven, with key enzymes co-occurring within MAGs from four previously unidentified phyla Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota. We informatically identify an additional group of high-affinity hydrogenases, group 1m [NiFe]-hydrogenase using phylogenetics, gene structure analysis and homology modelling and reveal substantial new genetic ersity within RuBisCO form IE ( rbcL1E ), and high-affinity groups 1h and 1l [NiFe]-hydrogenases. Finally, we conclude that atmospheric chemosynthesis is a global phenomenon, extending throughout and beyond cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental and clinical reservoirs.
Integrating ecology into biotechnology
Publisher: Elsevier BV
Date: 06-2007
DOI: 10.1016/J.COPBIO.2007.04.007
Abstract: New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a purely descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer systems that are biologically optimized for the desired goal. But to achieve this goal, ecology, engineering and microbiology curricula need to be changed from the very root to better promote interdisciplinarity.
Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment
Publisher: Cold Spring Harbor Laboratory
Date: 16-08-2019
DOI: 10.1101/737403
Abstract: Antibiotic resistance has emerged as a major global health threat. The Zn 2+ -dependent metallo-β-lactamases (MBLs) are of particular concern as they act on the most widely prescribed class of antibiotics, the β-lactams, and are largely unaffected by commonly used β-lactamase antagonists such as clavulanic acid. MBLs are sub ided into three groups (B1 to B3) despite low overall sequence similarity, their catalytic centers are conserved with two closely spaced Zn 2+ binding sites (α and β site). We recovered almost 1500 B3 MBLs from ,000 public microbial genomes representing a wide range of habitats including pristine sites not impacted by human activity. Although homologs were predominantly identified in members of the bacterial phylum Proteobacteria , the recovered B3 MBLs represent a much broader phylogenetic ersity than is currently appreciated based on the study of model pathogens. This includes three active site variants inferred to have arisen from the ancestral B3 enzyme. One of these variants, B3-RQK, is noteworthy for being broadly sensitive to clavulanic acid. Through targeted mutations we demonstrate that the presence of a lysine residue (Lys263) in the β site of the catalytic center of this variant confers sensitivity to this compound. Replacing this lysine with the canonical histidine (His263) found in all other MBLs restored resistance. Crystallographic and computational data reveal that clavulanic acid inhibits B3-RQK MBLs by displacing the Zn 2+ ion in the β site. Therefore, modifying clavulanic acid to effectively interact with His263 may increase the therapeutic range of this widely used antibiotic resistance drug. This study surveys the environmental and phylogenetic ersity of the B3 subgroup of antibiotic-degrading metallo-β-lactamases (MBLs). B3-like MBLs are more widespread in the environment than previously appreciated suggesting multiple unrecognized reservoirs of antibiotic resistance. Three variants of the canonical active site were identified, including B3-RQK, which amongst the B3 MBLs is uniquely inhibited by the antibiotic resistance drug clavulanic acid. We demonstrate that the mode of inhibition involves the displacement of a catalytically essential Zn 2+ ion from the active site. It may thus be possible to modify clavulanic acid so that it can compete with the Zn 2+ ions in other MBLs as well, increasing the therapeutic range of this compound.
Microbiomes in respiratory health and disease: An Asia-Pacific perspective
Publisher: Wiley
Date: 19-01-2017
DOI: 10.1111/RESP.12971
Abstract: There is currently enormous interest in studying the role of the microbiome in health and disease. Microbiome's role is increasingly being applied to respiratory diseases, in particular COPD, asthma, cystic fibrosis and bronchiectasis. The changes in respiratory microbiomes that occur in these diseases and how they are modified by environmental challenges such as cigarette smoke, air pollution and infection are being elucidated. There is also emerging evidence that gut microbiomes play a role in lung diseases through the modulation of systemic immune responses and can be modified by diet and antibiotic treatment. There are issues that are particular to the Asia-Pacific region involving diet and prevalence of specific respiratory diseases. Each of these issues is further complicated by the effects of ageing. The challenges now are to elucidate the cause and effect relationships between changes in microbiomes and respiratory diseases and how to translate these into new treatments and clinical care. Here we review the current understanding and progression in these areas.
Desiccation resistance of bacteria isolated from an air-handling system biofilm determined using a simple quantitative membrane filter method
Publisher: Oxford University Press (OUP)
Date: 07-1995
IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota
Publisher: BMJ
Date: 30-01-2019
DOI: 10.1136/ANNRHEUMDIS-2018-214381
Abstract: Certain gut bacterial families, including Bacteroidaceae, Porphyromonadaceae and Prevotellaceae, are increased in people suffering from spondyloarthropathy (SpA), a disease group associated with IL23R signalling variants. To understand the relationship between host interleukin (IL)-23 signalling and gut bacterial dysbiosis in SpA, we inhibited IL-23 in dysbiotic ZAP-70-mutant SKG mice that develop IL-23-dependent SpA-like arthritis, psoriasis-like skin inflammation and Crohn’s-like ileitis in response to microbial beta 1,3-glucan (curdlan). We treated SKG mice weekly with anti-IL-23 or isotype mAb for 3 weeks, rested them for 3 weeks, then administered curdlan or saline. We collected faecal s les longitudinally, assessed arthritis, spondylitis, psoriasis and ileitis histologically, and analysed the microbiota community profiles using next-generation sequencing. We used multivariate sparse partial least squares discriminant analysis to identify operational taxonomic unit (OTU) signatures best classifying treatment groups and linear regression to develop a predictive model of disease severity. IL-23p19 inhibition in naïve SKG mice decreased Bacteroidaceae, Porphyromonadaceae and Prevotellaceae. Abundance of Clostridiaceae and Lachnospiraceae families concomitantly increased, and curdlan-mediated SpA development decreased. Abundance of Enterobacteriaceae and Porphyromonadaceae family and reduction in Lachnospiraceae Dorea genus OTUs early in disease course were associated with disease severity in affected tissues. Dysbiosis in SKG mice reflects human SpA and is IL-23p19 dependent. In genetically susceptible hosts, IL-23p19 favours outgrowth of SpA-associated pathobionts and reduces support for homeostatic-inducing microbiota. The relative abundance of specific pathobionts is associated with disease severity.
Greengenes2 enables a shared data universe for microbiome studies
Publisher: Cold Spring Harbor Laboratory
Date: 20-12-2022
DOI: 10.1101/2022.12.19.520774
Abstract: 16S rRNA and shotgun metagenomics studies typically yield different results, usually attributed to biases in PCR lification of 16S rRNA genes. Here, we introduce Greengenes2 and show that differences in reference phylogeny are more important. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same s les agree in principal coordinates space, taxonomy, and in phenotype effect size when analyzed with the same tree.
STAMP: statistical analysis of taxonomic and functional profiles
Publisher: Oxford University Press (OUP)
Date: 23-07-2014
DOI: 10.1093/BIOINFORMATICS/BTU494
Abstract: Summary: STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparing pairs of s les or s les organized into two or more treatment groups. Effect sizes and confidence intervals are provided to allow critical assessment of the biological relevancy of test results. A user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots. Availability and implementation: STAMP is licensed under the GNU GPL. Python source code and binaries are available from our website at: kiwi.cs.dal.ca/Software/STAMP Contact: donovan.parks@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Corrigendum
Publisher: Oxford University Press (OUP)
Date: 15-10-2006
Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif
Publisher: Worldwide Protein Data Bank
Date: 25-12-2019
DOI: 10.2210/PDB6NC5/PDB
On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria
Publisher: American Association for the Advancement of Science (AAAS)
Date: 31-03-2017
Abstract: Oxygen-producing photosynthesis and oxygen-consuming respiration evolved after the ergence of the main lineages of blue-green algae.
Microvolume DNA extraction methods for microscale amplicon and metagenomic studies
Publisher: Springer Science and Business Media LLC
Date: 17-12-2021
DOI: 10.1038/S43705-021-00079-Z
Abstract: Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre s les, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we s led seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk s les (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both licon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise s ling of the heterogenous landscape that microbes inhabit.
Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas aeruginosa
Publisher: American Society for Microbiology
Date: 06-2007
DOI: 10.1128/JCM.02187-06
Abstract: Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial ersity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in s les from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa . PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial ersity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial ersity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli , suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial ersity may directly contribute to pathogen selection and persistence.
A complete domain-to-species taxonomy for Bacteria and Archaea (vol 58, pg 561, 2020)
Publisher: Springer Science and Business Media LLC
Date: 04-05-2020
Relative Time Inference Using Lateral Gene Transfers
Publisher: Springer US
Date: 2022
DOI: 10.1007/978-1-0716-2691-7_4
Abstract: Many organisms are able to incorporate exogenous DNA into their genomes. This process, called lateral gene transfer (LGT), has the potential to benefit the recipient organism by providing useful coding sequences, such as antibiotic resistance genes or enzymes which expand the organism's metabolic niche. For evolutionary biologists, LGTs have often been considered a nuisance because they complicate the reconstruction of the underlying species tree that many analyses aim to recover. However, LGT events between distinct organisms harbor information on the relative ergence time of the donor and recipient lineages. As a result transfers provide a novel and as yet mostly unexplored source of information to determine the order of ergence of clades, with the potential for absolute dating if linked to the fossil record.
Single Cell Whole Genome Amplification of Uncultivated Organisms
Publisher: Springer Berlin Heidelberg
Date: 2009
Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Publisher: Springer Science and Business Media LLC
Date: 04-2018
DOI: 10.1038/NBT0418-368C
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
Publisher: Frontiers Media SA
Date: 20-04-2021
DOI: 10.3389/FMICB.2021.643682
Abstract: A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal s les.
Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice
Publisher: BMJ
Date: 04-01-2021
DOI: 10.1136/ANNRHEUMDIS-2020-219009
Abstract: Analysis of oral dysbiosis in in iduals sharing genetic and environmental risk factors with rheumatoid arthritis (RA) patients may illuminate how microbiota contribute to disease susceptibility. We studied the oral microbiota in a prospective cohort of patients with RA, first-degree relatives (FDR) and healthy controls (HC), then genomically and functionally characterised streptococcal species from each group to understand their potential contribution to RA development. After DNA extraction from tongue swabs, targeted 16S rRNA gene sequencing and statistical analysis, we defined a microbial dysbiosis score based on an operational taxonomic unit signature of disease. After selective culture from swabs, we identified streptococci by sequencing. We examined the ability of streptococcal cell walls (SCW) from isolates to induce cytokines from splenocytes and arthritis in ZAP-70-mutant SKG mice. RA and FDR were more likely to have periodontitis symptoms. An oral microbial dysbiosis score discriminated RA and HC subjects and predicted similarity of FDR to RA. Streptococcaceae were major contributors to the score. We identified 10 out of 15 streptococcal isolates as S. parasalivarius sp. nov., a distinct sister species to S. salivarius . Tumour necrosis factor and interleukin 6 production in vitro differed in response to in idual S. parasalivarius isolates, suggesting strain specific effects on innate immunity. Cytokine secretion was associated with the presence of proteins potentially involved in S. parasalivarius SCW synthesis. Systemic administration of SCW from RA and HC-associated S. parasalivarius strains induced similar chronic arthritis. Dysbiosis-associated periodontal inflammation and barrier dysfunction may permit arthritogenic insoluble pro-inflammatory pathogen-associated molecules, like SCW, to reach synovial tissue.
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Publisher: Public Library of Science (PLoS)
Date: 19-07-2013
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores
Publisher: Proceedings of the National Academy of Sciences
Date: 28-07-2010
Abstract: Metagenomic and bioinformatic approaches were used to characterize plant biomass conversion within the foregut microbiome of Australia's “model” marsupial, the Tammar wallaby ( Macropus eugenii ). Like the termite hindgut and bovine rumen, key enzymes and modular structures characteristic of the “free enzyme” and “cellulosome” paradigms of cellulose solubilization remain either poorly represented or elusive to capture by shotgun sequencing methods. Instead, multigene polysaccharide utilization loci-like systems coupled with genes encoding β-1,4-endoglucanases and β-1,4-endoxylanases—which have not been previously encountered in metagenomic datasets—were identified, as were a erse set of glycoside hydrolases targeting noncellulosic polysaccharides. Furthermore, both rrs gene and other phylogenetic analyses confirmed that unique clades of the Lachnospiraceae, Bacteroidales, and Gammaproteobacteria are predominant in the Tammar foregut microbiome. Nucleotide composition-based sequence binning facilitated the assemblage of more than two megabase pairs of genomic sequence for one of the novel Lachnospiraceae clades (WG-2). These analyses show that WG-2 possesses numerous glycoside hydrolases targeting noncellulosic polysaccharides. These collective data demonstrate that Australian macropods not only harbor unique bacterial lineages underpinning plant biomass conversion, but their repertoire of glycoside hydrolases is distinct from those of the microbiomes of higher termites and the bovine rumen.
Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters
Publisher: Springer Science and Business Media LLC
Date: 17-04-2014
Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1GC15193B
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
Publisher: Springer Science and Business Media LLC
Date: 18-10-2007
Abstract: Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies. We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa. GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for ex le, database curation, microarray design and pangenome assignments. The application is available at the greengenes website [1].
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) (vol 13, pg 663, 2019)
Publisher: Springer Science and Business Media LLC
Date: 21-11-2020
Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere
Publisher: Springer Science and Business Media LLC
Date: 02-03-2015
DOI: 10.1038/SREP08678
Abstract: Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities in the rhizosphere is the result of complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent fungal community profiling, we have investigated the effects of nitrogen fertilizer dosage on fungal communities in soil and rhizosphere of field-grown sugarcane. The results show that the concentration of nitrogen fertilizer strongly modifies the composition but not the taxon richness of fungal communities in soil and rhizosphere. Increased nitrogen fertilizer dosage has a potential negative impact on carbon cycling in soil and promotes fungal genera with known pathogenic traits, uncovering a negative effect of intensive fertilization.
Towards understanding the taxonomy of some of the filamentous bacteria causing bulking and foaming in activated sludge plants
Publisher: IWA Publishing
Date: 1996
Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
Publisher: Springer Science and Business Media LLC
Date: 07-07-2016
Chemotaxis shapes the microscale organization of the ocean’s microbiome
Publisher: Springer Science and Business Media LLC
Date: 20-04-2022
DOI: 10.1038/S41586-022-04614-3
Abstract: The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
Publisher: Springer Science and Business Media LLC
Date: 17-12-2013
DOI: 10.4056/SIGS.5068949
CopyRighter: A rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
Publisher: Springer Science and Business Media LLC
Date: 07-04-2014
Effects of laboratory domestication on the rodent gut microbiome
Publisher: Springer Science and Business Media LLC
Date: 17-09-2021
DOI: 10.1038/S43705-021-00053-9
Abstract: The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal s les from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae , respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae , Streptococcaceae and Enterobacteriaceae , were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.
The power and limitations of species tree-aware phylogenetics
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2023
DOI: 10.1101/2023.03.17.533068
Abstract: Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For ex le, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress. Evolutionary trees provide a framework for understanding the history of life and organising bio ersity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.
Blastomonas Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a, 1117
Publisher: Springer-Verlag
Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif
Publisher: Worldwide Protein Data Bank
Date: 12-06-2019
DOI: 10.2210/PDB6DN4/PDB
GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2022
DOI: 10.1101/2022.07.11.499641
Abstract: The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (~320 GB) which limits its adoption and ease of use. Here we present an update to GTDB-Tk that uses a ide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: cogenomics/gtdbtk . p.chaumeil@uq.edu.au or donovan.parks@gmail.com
Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active-Site Glutamic Acid
Publisher: American Society for Microbiology
Date: 17-09-2021
DOI: 10.1128/AAC.00936-21
Abstract: The structural ersity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active-site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations were reported previously.
Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria
Publisher: American Society for Microbiology
Date: 07-2004
DOI: 10.1128/AEM.70.7.4363-4366.2004
Abstract: Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria , Verrucomicrobia , and Gemmatimonadetes and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.
Longitudinal Holistic Profiling of the Lung Transplant Microbiome
Publisher: Elsevier BV
Date: 04-2013
SeqCode: a nomenclatural code for prokaryotes described from sequence data
Publisher: Springer Science and Business Media LLC
Date: 19-09-2022
DOI: 10.1038/S41564-022-01214-9
Abstract: Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single- lified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide ex les for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
Building on basic metagenomics with complementary technologies
Publisher: Springer Science and Business Media LLC
Date: 2007
Emerging pathogenic links between microbiota and the gut-lung axis
Publisher: Springer Science and Business Media LLC
Date: 03-10-2017
Abstract: The microbiota is vital for the development of the immune system and homeostasis. Changes in microbial composition and function, termed dysbiosis, in the respiratory tract and the gut have recently been linked to alterations in immune responses and to disease development in the lungs. In this Opinion article, we review the microbial species that are usually found in healthy gastrointestinal and respiratory tracts, their dysbiosis in disease and interactions with the gut-lung axis. Although the gut-lung axis is only beginning to be understood, emerging evidence indicates that there is potential for manipulation of the gut microbiota in the treatment of lung diseases.
Genomic Analysis of “ Elusimicrobium minutum ,” the First Cultivated Representative of the Phylum “ Elusimicrobia ” (Formerly Termite Grou
Publisher: American Society for Microbiology
Date: 05-2009
DOI: 10.1128/AEM.02698-08
Abstract: Organisms of the candidate phylum termite group 1 (TG1) are regularly encountered in termite hindguts but are present also in many other habitats. Here, we report the complete genome sequence (1.64 Mbp) of “ Elusimicrobium minutum ” strain Pei191 T , the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut, and we discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE -like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, nonribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of “ Elusimicrobia ” (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.
Toward unrestricted use of public genomic data
Publisher: American Association for the Advancement of Science (AAAS)
Date: 25-01-2019
Abstract: Publication interests should not limit access to public data
The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities
Publisher: IWA Publishing
Date: 1998
A changing of the guard
Publisher: Wiley
Date: 03-2009
Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-12-2006
Abstract: Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)–based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16 S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16 S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of .006 cubic micrometer.
Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples
Publisher: Public Library of Science (PLoS)
Date: 13-04-2012
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-02-2007
Abstract: The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA–based approaches depending on the polymerase chain reaction. Mapping marker genes from four erse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
Publisher: American Society for Microbiology
Date: 15-09-1998
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Publisher: Springer Science and Business Media LLC
Date: 26-05-2013
DOI: 10.1038/NBT.2579
Abstract: Reference genomes are required to understand the erse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.
Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient
Publisher: Springer Science and Business Media LLC
Date: 25-05-2021
DOI: 10.1038/S41396-021-01001-0
Abstract: Desert soils harbour erse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their bio ersity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H 2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H 2 oxidation, chemosynthetic CO 2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H 2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome
Publisher: American Thoracic Society
Date: 15-03-2013
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Publisher: Springer Science and Business Media LLC
Date: 02-2018
DOI: 10.1038/NBT0218-196A
Crosstalk between sugarcane and a plant-growth promoting Burkholderia species
Publisher: Springer Science and Business Media LLC
Date: 21-11-2016
DOI: 10.1038/SREP37389
Abstract: Bacterial species in the plant-beneficial-environmental clade of Burkholderia represent a substantial component of rhizosphere microbes in many plant species. To better understand the molecular mechanisms of the interaction, we combined functional studies with high-resolution dual transcriptome analysis of sugarcane and root-associated diazotrophic Burkholderia strain Q208. We show that Burkholderia Q208 forms a biofilm at the root surface and suppresses the virulence factors that typically trigger immune response in plants. Up-regulation of bd -type cytochromes in Burkholderia Q208 suggests an increased energy production and creates the microaerobic conditions suitable for BNF. In this environment, a series of metabolic pathways are activated in Burkholderia Q208 implicated in oxalotrophy, microaerobic respiration, and formation of PHB granules, enabling energy production under microaerobic conditions. In the plant, genes involved in hypoxia survival are up-regulated and through increased ethylene production, larger aerenchyma is produced in roots which in turn facilitates diffusion of oxygen within the cortex. The detected changes in gene expression, physiology and morphology in the partnership are evidence of a sophisticated interplay between sugarcane and a plant-growth promoting Burkholderia species that advance our understanding of the mutually beneficial processes occurring in the rhizosphere.
Draft Genome Sequence of Limisphaera ngatamarikiensis NGM72.4 T , a Moderately Alkaliphilic Thermophile Belonging to the Class Verrucomicrobiae
Publisher: American Society for Microbiology
Date: 30-04-2020
DOI: 10.1128/MRA.00225-20
Abstract: Limisphaera ngatamarikiensis NGM72.4 T is a thermophilic representative of the class Verrucomicrobiae . Isolated from geothermally heated subaqueous clay sediments from a Ngatamariki hotspring in Aotearoa New Zealand, the 3,908,748-bp genome was sequenced using the Illumina HiSeq 2500 platform. Annotation revealed 3,083 coding sequences, including 3,031 proteins, 3 rRNA genes, and 46 tRNA genes.
Discovery of a novel methanogen prevalent in thawing permafrost
Publisher: Springer Science and Business Media LLC
Date: 14-02-2014
DOI: 10.1038/NCOMMS4212
Abstract: Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.
Draft Genome Sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, Previously Desc
Publisher: American Society for Microbiology
Date: 29-10-2015
Abstract: Members of the class Anaerolineae in the bacterial phylum Chloroflexi are widespread in a range of ecosystems but remain poorly understood. We present here the draft genome sequences of the type strains of five Anaerolineae species, Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tar italis YMTK-2, Levilinea saccharolytica KIBI-1, and Longilinea arvoryzae KOME-1.
A rooted phylogeny resolves early bacterial evolution
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-05-2021
Abstract: The origin of the eubacteria and phylogenetic relationships between subgroups have been difficult to resolve. Applying a phylogenetic analysis and recent computational methods to the expanded ersity of bacterial sequences from metagenomic analyses, Coleman et al. infer the root of the eubacterial tree (see the Perspective by Katz). The root was determined without using the Archaea as an outgroup, to avoid the possibility of a false result due to long branch attraction. This method places the eubacterial root in the neighborhood of Fusobacteriota. Using this information, the authors reconstructed the eubacterial ancestor, identifying that this organism likely had a double-membrane cell envelope, flagellum-mediated motility, antiphage defense mechanisms, and erse metabolic pathways. Science , this issue p. eabe0511 see also p. 574
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
Publisher: Springer Science and Business Media LLC
Date: 12-2011
A complete domain-to-species taxonomy for Bacteria and Archaea
Publisher: Springer Science and Business Media LLC
Date: 27-04-2020
DOI: 10.1038/S41587-020-0501-8
Abstract: The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural 'type' defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.
Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows
Publisher: Springer Science and Business Media LLC
Date: 22-09-2011
Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies
Publisher: American Association for the Advancement of Science (AAAS)
Date: 29-07-2011
Abstract: Metagenome sequence predicted the culture conditions required for successful isolation of a marsupial gut bacterium.
Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors
Publisher: American Society for Microbiology
Date: 05-1995
DOI: 10.1128/AEM.61.5.1910-1916.1995
Abstract: The bacterial community structures of phosphate- and non-phosphate-removing activated sludges were compared. Sludge s les were obtained from two sequencing batch reactors (SBRs), and 16S rDNA clone libraries of the bacterial sludge populations were established. Community structures were determined by phylogenetic analyses of 97 and 92 partial clone sequences from SBR1 (phosphate-removing sludge) and SBR2 (non-phosphate-removing sludge), respectively. For both sludges, the predominant bacterial group with which clones were affiliated was the beta subclass of the proteobacteria. Other major groups represented were the alpha proteobacterial subclass, planctomycete group, and Flexibacter-Cytophaga-Bacteroides group. In addition, several clone groups unaffiliated with known bacterial assemblages were identified in the clone libraries. Acinetobacter spp., thought to be important in phosphate removal in activated sludge, were poorly represented by clone sequences in both libraries. Differences in community structure were observed between the phosphate- and non-phosphate-removing sludges in particular, the Rhodocyclus group within the beta subclass was represented to a greater extent in the phosphate-removing community. Such differences may account for the differing phosphate-removing capabilities of the two activated sludge communities.
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
Publisher: Oxford University Press (OUP)
Date: 11-10-2022
DOI: 10.1093/BIOINFORMATICS/BTAC672
Abstract: The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a ide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: cogenomics/gtdbtk. Supplementary data are available at Bioinformatics online.
Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon
Publisher: American Society for Microbiology
Date: 1997
DOI: 10.1128/AEM.63.1.254-262.1997
Abstract: Bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain Bacteria were isolated from postlarvae of the giant tiger prawn, Penaeus monodon. A selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. Planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. The predominant colony type recovered from postlarvae regardless of viral infection status was nonpigmented. Other, less commonly observed types were pink or orange pigmented. A planctomycete-specific 16S rRNA-directed probe was designed and used to screen the isolates for their identity as planctomycetes prior to molecular phylogenetic characterization. 16S rRNA genes from nine prawn isolates together with two planctomycete reference strains (Planctomyces brasiliensis and Gemmata obscuriglobus) were sequenced and compared with reference sequences from the planctomycetes and other members of the domain Bacteria. Phylogenetic analyses and sequence signatures of the 16S rRNA genes demonstrated that the prawn isolates were members of the planctomycete group. Five representatives of the predominant nonpigmented colony type were members of the Pirellula group within the planctomycetes, as were three pink-pigmented colony type representatives. Homology values and tree topology indicated that representatives of the nonpigmented and pink-pigmented colony types formed two discrete clusters within the Pirellula group, not identical to any known Pirellula species. A sole representative of the orange colony type was a member of the Planctomyces group, virtually identical in 16S rDNA sequence to P. brasiliensis, and exhibited distinctive morphology.
In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth
Publisher: Wiley
Date: 07-2002
DOI: 10.1046/J.1462-2920.2002.00316.X
Abstract: Among the filamentous bacteria occasionally causing bulking problems in activated sludge treatment plants, three morphotypes with attached microbial growth are common, Eikelboom Type 0041, Type 1851 and Type 1701. A better knowledge of the phylogeny and physiology of these filamentous bacteria is necessary in order to develop control strategies for bulking. In this study we have used a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) to investigate the identity and in situ physiology of the Type 0041-morphotype and its attached bacteria in two wastewater treatment plants. Identification and enumeration of Type 0041 using group-specific 16S rRNA-targeted FISH probes revealed that approximately 15% of the filaments hybridized with a gene probe specific for the TM7 group, a recently recognized major lineage in the bacterial domain. All other filaments morphologically identified as Type 0041 only hybridized to the general bacterial EUB338-probe, indicating that they probably do not belong to commonly isolated bacterial phyla such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, for which group-specific probes were used. The phylogenetic heterogeneity of Type 0041 again highlights the inadequacy of a morphology-based classification system. Like the filaments, most of the attached microbial cells were not identified beyond their affiliation to the Bacteria using the group-specific FISH probes. However, several different bacterial phyla were represented in the identified fraction suggesting that the attached microorganisms are phylogenetically erse. The study of the in situ physiology of Type 0041 using MAR-FISH revealed that both the filaments and the attached bacteria on Type 0041 were versatile in the use of organic substrates and electron acceptors. It was observed that all Type 0041 could consume glucose, but none of the filaments were able to consume acetate under any conditions tested, in contrast to some of the attached bacteria. No significant physiological differences were found between TM7-positive and TM7-negative Type 0041 filaments, and only minor differences were observed between the two treatment plants tested. These are the first data on the physiology of the almost entirely uncharacterized TM7 phylum and show that TM7 filamentous bacteria can uptake carbon substrates under aerobic and anaerobic conditions.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Publisher: Springer Science and Business Media LLC
Date: 08-2017
DOI: 10.1038/NBT.3893
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal ersity.
Focus: Synergistetes
Publisher: Wiley
Date: 31-05-2009
A korarchaeal genome reveals insights into the evolution of the Archaea
Publisher: Proceedings of the National Academy of Sciences
Date: 10-06-2008
Abstract: The candidate ision Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have erged early from the major archaeal phyla Crenarchaeota and Euryarchaeota . Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, “ Candidatus Korarchaeum cryptofilum,” which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota . However, the predicted gene content revealed that several conserved cellular systems, such as cell ision, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota . In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.
Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages
Publisher: Cold Spring Harbor Laboratory
Date: 19-02-2021
DOI: 10.1101/2021.02.19.431964
Abstract: Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative organoheterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including deep subsurface, shallow lake, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four novel lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Hodarchaeia class nov. and Cand. Jordarchaeia class nov., derived from the gods Hod and Jord in Norse mythology. Metabolic inference suggests that both novel classes represent methylotrophic acetogens, encoding the transfer of methyl groups, such as methylated amines, to coenzyme M with acetate as the end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e. recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding on the other hand is restricted to Hodarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic lineage with an inferred complete Pyl machinery, likely providing this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of Bacteria and Eukaryotes, in both novel classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
Blastobacter
Publisher: Wiley
Date: 14-09-2015
DOI: 10.1002/9781118960608.GBM00800
Abstract: Blas.to.bac' ter . Gr. n. blastos bud, shoot M.L. n. bacter equivalent of Gr. masc. n. bactrum rod M.L. masc. n. Blastobacter a budding rod. Proteobacteria / Alphaproteobacteria / Rhizobiales / Bradyrhizobiaceae / Blastobacter Cells ovoid rods , wedge or club shaped , or pleomorphic, often slightly curved and occasionally branched . Cell poles are rounded or slightly tapering on one pole. Cell size range is 0.5–1.0 × 1.0–4.5 µm. Cells may form rosettes . Gram negative . New cell formation and multiplication occur by budding on the free cell pole, subpolarly or laterally. Young buds initially rod shaped , ovoid , or spherical to oblong . Buds may be released or remain attached. Motile , flagellated swarmer cells may occur in some species. Do not form spores or cysts. Some strains produce large amounts of exopolymer. Grow in liquids as turbidity, pellicle, or precipitate. Colony pigmentation may be yellow, or colorless, becoming brown in older cultures. The mol % G + C of the DNA is : 59–69. Type species : Blastobacter henricii Zavarzin 1961, 962.
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Publisher: Oxford University Press (OUP)
Date: 2006
DOI: 10.1093/NAR/GKJ145
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
Publisher: Springer Science and Business Media LLC
Date: 05-08-2010
Skin Cancer-Associated S. aureus Strains Can Induce DNA Damage in Human Keratinocytes by Downregulating DNA Repair and Promoting Oxidative Stress
Publisher: MDPI AG
Date: 25-04-2022
Abstract: Actinic keratosis (AK) is a premalignant lesion, common on severely photodamaged skin, that can progress over time to cutaneous squamous cell carcinoma (SCC). A high bacterial load of Staphylococcus aureus is associated with AK and SCC, but it is unknown whether this has a direct impact on skin cancer development. To determine whether S. aureus can have cancer-promoting effects on skin cells, we performed RNA sequencing and shotgun proteomics on primary human keratinocytes after challenge with sterile culture supernatant (‘secretome’) from four S. aureus clinical strains isolated from AK and SCC. Secretomes of two of the S. aureus strains induced keratinocytes to overexpress biomarkers associated with skin carcinogenesis and upregulated the expression of enzymes linked to reduced skin barrier function. Further, these strains induced oxidative stress markers and all secretomes downregulated DNA repair mechanisms. Subsequent experiments on an expanded set of lesion-associated S. aureus strains confirmed that exposure to their secretomes led to increased oxidative stress and DNA damage in primary human keratinocytes. A significant correlation between the concentration of S. aureus phenol soluble modulin toxins in secretome and the secretome-induced level of oxidative stress and genotoxicity in keratinocytes was observed. Taken together, these data demonstrate that secreted compounds from lesion-associated clinical isolates of S. aureus can have cancer-promoting effects in keratinocytes that may be relevant to skin oncogenesis.
The minimum information about a genome sequence (MIGS) specification
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1038/NBT1360
Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence
Publisher: Springer Science and Business Media LLC
Date: 09-08-2017
DOI: 10.1038/S41467-017-00262-8
Abstract: Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene licon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium , and Burkholderia , and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.
Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy
Publisher: Cold Spring Harbor Laboratory
Date: 18-09-2019
DOI: 10.1101/771964
Abstract: We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914 de novo species clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results.
Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives
Publisher: American Society for Microbiology
Date: 2001
DOI: 10.1128/AEM.67.1.411-419.2001
Abstract: A molecular approach was used to investigate a recently described candidate ision of the domain Bacteria , TM7, currently known only from environmental 16S ribosomal DNA sequence data. A number of TM7-specific primers and probes were designed and evaluated. Fluorescence in situ hybridization (FISH) of a laboratory scale bioreactor using two independent TM7-specific probes revealed a conspicuous sheathed-filament morphotype, fortuitously enriched in the reactor. Morphologically, the filament matched the description of the Eikelboom morphotype 0041-0675 widely associated with bulking problems in activated-sludge wastewater treatment systems. Transmission electron microscopy of the bioreactor sludge demonstrated that the sheathed-filament morphotype had a typical gram-positive cell envelope ultrastructure. Therefore, TM7 is only the third bacterial lineage recognized to have gram-positive representatives. TM7-specific FISH analysis of two full-scale wastewater treatment plant sludges, including the one used to seed the laboratory scale reactor, indicated the presence of a number of morphotypes, including sheathed filaments. TM7-specific PCR clone libraries prepared from the two full-scale sludges yielded 23 novel TM7 sequences. Three sub isions could be defined based on these data and publicly available sequences. Environmental sequence data and TM7-specific FISH analysis indicate that members of the TM7 ision are present in a variety of terrestrial, aquatic, and clinical habitats. A highly atypical base substitution ( Escherichia coli position 912 C to U) for bacterial 16S rRNAs was present in almost all TM7 sequences, suggesting that TM7 bacteria, like Archaea , may be streptomycin resistant at the ribosome level.
Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif mutant S60
Publisher: Worldwide Protein Data Bank
Date: 12-06-2019
DOI: 10.2210/PDB6DQ2/PDB
Microorganisms should be high on DNA preservation list
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-11-2000
Erratum: Introducing BASE: The Biomes of Australian Soil Environments soil microbial diversity database [GigaScience. 5, 1, (2016) (1-11)] DOI: 10.1186/s13742-016-0126-5
Publisher: Oxford University Press (OUP)
Date: 05-2017
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
Publisher: Springer Science and Business Media LLC
Date: 21-01-2010
Abstract: Pyrosequencing of 16S rRNA gene licons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple s les in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of licon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using licons ranging in length from 352 to 1443 bp. Our results show that both licon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing ersity estimates across communities.
Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community
Publisher: American Society for Microbiology
Date: 2004
DOI: 10.1128/AEM.70.1.588-596.2004
Abstract: A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO 3 − -N mg of mixed-liquor volatile suspended solids (MLVSS) −1 h −1 to a steady-state value of 0.06 mg of NO 3 − -N mg of MLVSS −1 h −1 over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [ 13 C]methanol to biomark the DNA of the denitrifiers. The extracted [ 13 C]DNA and [ 12 C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [ 13 C]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [ 12 C]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [ 14 C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.
A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes
Publisher: Springer Science and Business Media LLC
Date: 25-02-2015
Author Correction: Roadmap for naming uncultivated Archaea and Bacteria
Publisher: Springer Science and Business Media LLC
Date: 12-11-2020
DOI: 10.1038/S41564-020-00827-2
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Blastomonas
Publisher: Wiley
Date: 14-09-2015
DOI: 10.1002/9781118960608.GBM00918
Abstract: Blas.to.mo' nas . Gr. n. blastos bud shoot Gr. n. monas a unit, monad M.L. fem. n. Blastomonas a budding monad. Proteobacteria / Alphaproteobacteria / Sphingomonadales / Sphingomonadaceae / Blastomonas Cells are ovoid or rod‐shaped and reproduce by budding or asymmetric cell ision . They occur singly or in pairs and may form rosette‐like aggregates . No stalks and prosthecae are found. Gram negative . Nonsporeforming. Motile by means of polar flagella . Strictly aerobic . Chemoorganotroph and facultative photoorganoheterotroph . No growth occurs under anaerobic conditions in the light. Produces BChl a . Colonies and cell suspensions are yellow to orange due to carotenoids . Mesophilic and neutrophilic . Catalase and oxidase positive . Nitrate is not reduced. Acid is not produced in Hugh and Leifson's OF medium. The major whole‐cell fatty acid is C 18 : 1 ω 9 . The major hydroxy‐fatty acid is C 14 : 0 2OH . C 15:0 2OH and C 16:0 2OH are present as minor components. 3‐OH fatty acids are absent. Monosaccharide‐type glycosphingolipids are present. Ubiquinone‐10 is the major respiratory quinone . Belongs to the Alphaproteobacteria . Habitat is fresh water. The mol % G + C of the DNA is : 65. Type species : Blastomonas natatoria (Sly 1985) Sly and Cahill 1997, 568 emend. Hiraishi, Kuraishi and Kawahara 2000a, 1117 ( Blastobacter natatorius Sly 1985, 43.)
Defining the human gut host–phage network through single-cell viral tagging
Publisher: Springer Science and Business Media LLC
Date: 05-08-2019
DOI: 10.1038/S41564-019-0526-2
Abstract: Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then in idually sorted as host-phage pairs, followed by genome lification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple in idual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Publisher: Springer Science and Business Media LLC
Date: 12-06-2017
DOI: 10.1038/NBT.3886
Abstract: We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic ersity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic ersity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 s les, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a ergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
Atmospheric trace gases support primary production in Antarctic desert surface soil
Publisher: Springer Science and Business Media LLC
Date: 12-2017
DOI: 10.1038/NATURE25014
Abstract: Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H
Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended des
Publisher: Microbiology Society
Date: 11-2004
Abstract: Sphaerobacter thermophilus was originally classified as the deepest branching member of the phylum Actinobacteria (high-G+C, Gram-positive bacteria) based on 16S rRNA gene comparative analysis. However, the analysis lacked suitable outgroups, and additional 16S rRNA gene sequences indicate that it is most closely related to Thermomicrobium roseum , which it also resembles phenotypically. Furthermore, both species are reproducibly affiliated with the phylum Chloroflexi (green non-sulfur bacteria), despite T. roseum currently being classified in its own phylum, the Thermomicrobia . Transfer of Sphaerobacter to the class Thermomicrobia , and transfer of the class Thermomicrobia to the phylum Chloroflexi , are proposed. Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification.
Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean
Publisher: Springer Science and Business Media LLC
Date: 08-2022
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Publisher: Springer Science and Business Media LLC
Date: 06-07-2018
DOI: 10.1038/NBT0718-660A
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
Publisher: American Society for Microbiology
Date: 15-08-2011
DOI: 10.1128/AEM.00032-11
Abstract: Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene licon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low- ersity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus , and Thermus thermophilus . At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging
Publisher: American Society for Microbiology
Date: 03-2013
Exploring prokaryotic diversity in the genomic era
Publisher: Springer Science and Business Media LLC
Date: 2002
DOI: 10.1186/GB-2002-3-2-REVIEWS0003
Abstract: Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced s ling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental s les.
A rooted phylogeny resolves early bacterial evolution
Publisher: Cold Spring Harbor Laboratory
Date: 15-07-2020
DOI: 10.1101/2020.07.15.205187
Abstract: Bacteria are the most abundant and metabolically erse cellular lifeforms on Earth. A rooted bacterial phylogeny provides a framework to interpret this ersity and to understand the nature of early life. Inferring the position of the bacterial root is complicated by incomplete taxon s ling and the long branch to the archaeal outgroup. To circumvent these limitations, we model bacterial genome evolution at the level of gene duplication, transfer and loss events, allowing outgroup-free inference of the root 1 . We infer a rooted bacterial tree on which 68% of gene transmission events are vertical. Our analyses reveal a basal split between Terrabacteria and Gracilicutes, which together encompass almost all known bacterial ersity. However, the position of one phylum, Fusobacteriota, could not be resolved in relation to these two major clades. In contrast to recent proposals, our analyses strongly reject a root between the Candidate Phyla Radiation (CPR) and all other Bacteria. Instead, we find that the CPR is a sister lineage to the Chloroflexota within the Terrabacteria. We predict that the last bacterial common ancestor was a free-living flagellated, rod-shaped cell featuring a double membrane with a lipopolysaccharide outer layer, a Type III CRISPR-Cas system, Type IV pili, and the ability to sense and respond via chemotaxis.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Publisher: Cold Spring Harbor Laboratory
Date: 14-05-2015
Abstract: Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional ersity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a erse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
Consent insufficient for data release—Response
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-05-2019
Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845T)
Publisher: Springer Science and Business Media LLC
Date: 29-04-2011
DOI: 10.4056/SIGS.1553865
Effects of sample treatments on genome recovery via single-cell genomics
Publisher: Springer Science and Business Media LLC
Date: 13-06-2014
DIETARY FIBRE AND MICROBIAL METABOLITES PROTECT AGAINST CIGARETTE SMOKE‐INDUCED LUNG PATHOLOGY IN MICE
Publisher: Wiley
Date: 11-2017
DOI: 10.1111/RESP.13206_3
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Publisher: PeerJ
Date: 27-01-2015
DOI: 10.7717/PEERJ.740
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Start Date: 2015
End Date: 2017
Funder: Australian Research Council
View Funded ActivityToward A Complete View Of Life On Earth Via Single Cell Genomics
Start Date: 2012
End Date: 2014
Funder: Australian Research Council
View Funded ActivityReconstructing The Universal Tree And Network Of Life
Start Date: 2015
End Date: 2019
Funder: Australian Research Council
View Funded ActivityRapid Functional And Taxonomic Skin Microbe Characterisation
Start Date: 2016
End Date: 2018
Funder: Australian Research Council
View Funded ActivityUnderstanding The Koala Microbiome: Koala Health And Dietary Specialisation, And Successful Husbandry And Translocation
Start Date: 2014
End Date: 2017
Funder: Australian Research Council
View Funded ActivityVolumetric Imaging Facility: Observing The Cell In Its Native Environment
Start Date: 2019
End Date: 2019
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP140100751
Start Date: 04-2015
End Date: 11-2018
Amount: $355,000.00
Funder: Australian Research Council
View Funded ActivityAustralian Laureate Fellowships - Grant ID: FL150100038
Start Date: 08-2015
End Date: 12-2021
Amount: $2,982,714.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP200101980
Start Date: 2020
End Date: 06-2024
Amount: $785,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP120103498
Start Date: 2012
End Date: 12-2015
Amount: $870,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP150104202
Start Date: 2015
End Date: 12-2018
Amount: $374,300.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP120200837
Start Date: 03-2013
End Date: 03-2018
Amount: $529,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP220100900
Start Date: 07-2022
End Date: 06-2025
Amount: $960,385.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE190100130
Start Date: 2019
End Date: 12-2019
Amount: $1,480,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP160100731
Start Date: 12-2016
End Date: 12-2019
Amount: $388,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP190100975
Start Date: 12-2020
End Date: 12-2024
Amount: $777,172.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE120100025
Start Date: 03-2012
End Date: 03-2013
Amount: $380,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Infrastructure, Equipment And Facilities - Grant ID: LE230100128
Start Date: 02-2023
End Date: 02-2024
Amount: $1,078,770.00
Funder: Australian Research Council
View Funded Activity