ORCID Profile
0000-0002-6151-190X
Current Organisations
Aalborg Universitet
,
Aalborg University
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Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.COPBIO.2019.03.008
Abstract: We have critically assessed some of the dogmas in the microbiology of enhanced biological phosphorus removal (EBPR) and argue that the genus Tetrasphaera can be as important as Ca. Accumulibacter for phosphorus removal and that proliferation of their competitors, the glycogen accumulating organisms, does not appear to be a practical problem for EBPR efficiency even under tropical conditions. An increasing number of EBPR-related genomes are changing our understanding of their physiology, for ex le, their potential to participate in denitrification. Rather than trying to identify organisms that adhere to strict phenotype metabolic models, we advocate for broader analyses of the whole microbial communities in EBPR plants by iterative studies with isolates, lab enrichments, and full-scale systems.
Publisher: Public Library of Science (PLoS)
Date: 04-09-0021
Publisher: Public Library of Science (PLoS)
Date: 15-09-0009
Publisher: Springer Science and Business Media LLC
Date: 28-02-2013
DOI: 10.1038/ISMEJ.2013.6
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.
Publisher: Oxford University Press (OUP)
Date: 2017
Publisher: Springer Science and Business Media LLC
Date: 2018
DOI: 10.1038/NBT.4045
Abstract: Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial ersity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the ersity present in a s le. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput. We apply our approach to s les from seven different ecosystems and obtain more than a million SSU rRNA sequences from all domains of life, with an estimated raw error rate of 0.17%. We observe a large proportion of novel ersity, including several deeply branching phylum-level lineages putatively related to the Asgard Archaea. Our approach will enable expansion of the SSU rRNA reference databases by orders of magnitude, and contribute to a comprehensive census of the tree of life.
Publisher: Cold Spring Harbor Laboratory
Date: 23-09-2022
DOI: 10.1101/2022.09.23.509140
Abstract: Marine sponges are critical components of marine benthic fauna assemblages where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, erse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont ‘ Candidatus Taurinisymbion ianthellae’ residing in the marine sponge, Ianthella basta , expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. ‘ Candidatus Taurinisymbion ianthellae’ incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont ‘ Candidatus Nitrosospongia ianthellae’. Metaproteogenomic analyses also indicate that ‘ Candidatus Taurinisymbion ianthellae’ likely imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
Publisher: American Society for Microbiology
Date: 27-10-2020
Abstract: High-throughput 16S rRNA gene licon sequencing is an essential method for studying the ersity and dynamics of microbial communities. However, this method is presently h ered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene licon sequence variant (FL-ASV) resolved reference databases that include high-identity references ( .
Publisher: Wiley
Date: 25-07-2019
Publisher: Springer Science and Business Media LLC
Date: 28-11-2022
DOI: 10.1038/S41564-022-01266-X
Abstract: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and h ers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a erse set of 880 microbial community s les collected for the Earth Microbiome Project. We include licon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore ersity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite ersity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for ex le, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from erse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
Publisher: Frontiers Media SA
Date: 27-04-2017
Publisher: Springer Science and Business Media LLC
Date: 18-10-2023
Publisher: Springer Science and Business Media LLC
Date: 31-10-2017
Publisher: American Society for Microbiology
Date: 25-06-2015
Abstract: Here, we present the complete genome sequence of the candidate phylum SR1 bacterium Aalborg_AAW-1. Its 16S rRNA gene is only 85.5% similar to that of the closest relative, RAAC1_SR1, and the genome of Aalborg_AAW-1 consequently represents the first of a novel family within the candidate phylum SR1.
Publisher: Springer Science and Business Media LLC
Date: 08-04-2016
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2017
DOI: 10.1101/207811
Abstract: Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an OTU belonging to Acetothermia was detected at high abundance in two full-scale anaerobic digesters. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with nanopore data. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtain energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.
Publisher: IWA Publishing
Date: 06-2013
DOI: 10.2166/WST.2013.151
Abstract: Since 2006 more than 50 Danish full-scale wastewater treatment plants with nutrient removal have been investigated in a project called ‘The Microbial Database for Danish Activated Sludge Wastewater Treatment Plants with Nutrient Removal (MiDas-DK)’. Comprehensive sets of s les have been collected, analyzed and associated with extensive operational data from the plants. The community composition was analyzed by quantitative fluorescence in situ hybridization (FISH) supported by 16S rRNA licon sequencing and deep metagenomics. MiDas-DK has been a powerful tool to study the complex activated sludge ecosystems, and, besides many scientific articles on fundamental issues on mixed communities encompassing nitrifiers, denitrifiers, bacteria involved in P-removal, hydrolysis, fermentation, and foaming, the project has provided results that can be used to optimize the operation of full-scale plants and carry out trouble-shooting. A core microbial community has been defined comprising the majority of microorganisms present in the plants. Time series have been established, providing an overview of temporal variations in the different plants. Interestingly, although most microorganisms were present in all plants, there seemed to be plant-specific factors that controlled the population composition thereby keeping it unique in each plant over time. Statistical analyses of FISH and operational data revealed some correlations, but less than expected. MiDas-DK (www.midasdk.dk) will continue over the next years and we hope the approach can inspire others to make similar projects in other parts of the world to get a more comprehensive understanding of microbial communities in wastewater engineering.
Publisher: Frontiers Media SA
Date: 23-06-2017
Publisher: Oxford University Press (OUP)
Date: 2015
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.
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.
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.SYAPM.2018.08.001
Abstract: Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, sometimes reaching abundances in excess of 30% of the biovolume. The uncultured Chloroflexi phylotype, Candidatus Amarolinea, has been observed in high abundances in Danish full-scale activated sludge systems by 16S rRNA gene licon surveys, where it has been associated with bulking. In this study, fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and contribution to the interfloc bridging that characterizes filamentous bulking. Furthermore, genome-centric metagenomics using both Illumina and Oxford Nanopore sequencing was used to obtain a near complete population genome (5.7Mbp) of the Ca. Amarolinea phylotype, which belongs to the proposed novel family Amarolineaceae within the order Caldilineales of Chloroflexi. Annotation of the genome indicated that the phylotype is capable of aerobic respiration, fermentation, and dissimilatory nitrate reduction to ammonia. The genome sequence also gives a better insight into the phylogenetic and evolutionary relationships of the organism. The name Candidatus Amarolinea aalborgensis is proposed for the species.
Publisher: Springer Science and Business Media LLC
Date: 24-08-2017
DOI: 10.1038/S41598-017-09303-0
Abstract: Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. Hence, we investigated microbial communities of thirty-two full-scale anaerobic digesters over a six-year period using 16S rRNA gene licon sequencing. S ling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the growing microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable and comparison to other studies problematic. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of in idual digesters surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as non-growing and possibly inactive immigrating microbes. By identifying abundant and growing taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process-important organisms towards an in-depth understanding of the microbiology.
Publisher: Cold Spring Harbor Laboratory
Date: 31-01-2017
DOI: 10.1101/104620
Abstract: Anaerobic digestion is widely applied to treat organic waste at wastewater treatment plants. Characterisation of the underlying microbiology represents a source of information to develop strategies for improved operation. To this end, we investigated the microbial community composition of thirty-two full-scale digesters over a six-year period using 16S rRNA gene licon sequencing. S ling of the sludge fed into these systems revealed that several of the most abundant populations were likely inactive and immigrating with the influent. This observation indicates that a failure to consider immigration will interfere with correlation analysis and give an inaccurate picture of the active microbial community. Furthermore, several abundant OTUs could not be classified to genus level with commonly applied taxonomies, making inference of their function unreliable. As such, the existing MiDAS taxonomy was updated to include these abundant phylotypes. The communities of in idual plants surveyed were remarkably similar – with only 300 OTUs representing 80% of the total reads across all plants, and 15% of these identified as likely inactive immigrating microbes. By identifying the abundant and active taxa in anaerobic digestion, this study paves the way for targeted characterisation of the process important organisms towards an in-depth understanding of the microbial ecology of these biotechnologically important systems.
Publisher: Springer Science and Business Media LLC
Date: 23-02-2016
Publisher: Springer Science and Business Media LLC
Date: 31-10-2014
Publisher: IWA Publishing
Date: 19-10-2013
DOI: 10.2166/WST.2013.441
Abstract: Metagenomics enables studies of the genomic potential of complex microbial communities by sequencing bulk genomic DNA directly from the environment. Knowledge of the genetic potential of a community can be used to formulate and test ecological hypotheses about stability and performance. In this study deep metagenomics and fluorescence in situ hybridization (FISH) were used to study a full-scale wastewater treatment plant with enhanced biological phosphorus removal (EBPR), and the results were compared to an existing EBPR metagenome. EBPR is a widely used process that relies on a complex community of microorganisms to function properly. Insight into community and species level stability and dynamics is valuable for knowledge-driven optimization of the EBPR process. The metagenomes of the EBPR communities were distinct compared to metagenomes of communities from a wide range of other environments, which could be attributed to selection pressures of the EBPR process. The metabolic potential of one of the key microorganisms in the EPBR process, Accumulibacter, was investigated in more detail in the two plants, revealing a potential importance of phage predation on the dynamics of Accumulibacter populations. The results demonstrate that metagenomics can be used as a powerful tool for system wide characterization of the EBPR community as well as for a deeper understanding of the function of specific community members. Furthermore, we discuss and illustrate some of the general pitfalls in metagenomics and stress the need of additional DNA extraction independent information in metagenome studies.
Publisher: Frontiers Media SA
Date: 04-07-2016
Publisher: Cold Spring Harbor Laboratory
Date: 22-08-2016
DOI: 10.1101/070771
Abstract: Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial ersity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies. However, the underlying reference databases of full-length rRNA gene sequences are underpopulated, ecosystem skewed 1 , and subject to primer bias 2 , which h er our ability to study the true ersity of ecosystems. Here we present an approach that combines reverse transcription of full-length small subunit (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity). For the Eukaryotes, the novelty was even larger with 63% of all OTUs representing novel taxa. In addition, 15% of the 18S rRNA OTUs were highly novel sequences with less than 80% similarity to the databases. The generation of primer-free full-length SSU rRNA sequences enabled eco-system specific estimation of primer-bias and, especially for eukaryotes, showed a dramatic discrepancy between the in-silico evaluation and primer-free data generated in this study. The large amount of novel sequences obtained here reaffirms that there is still vast, untapped microbial ersity lacking representatives in the SSU rRNA databases and that there might be more than millions after all 1, 3 . With our new approach, it is possible to readily expand the rRNA databases by orders of magnitude within a short timeframe. This will, for the first time, enable a broad census of the tree of life.
Publisher: Springer Science and Business Media LLC
Date: 15-12-2012
Publisher: Springer Science and Business Media LLC
Date: 11-08-2015
Publisher: Springer Science and Business Media LLC
Date: 08-06-2018
Publisher: Cold Spring Harbor Laboratory
Date: 18-06-2019
DOI: 10.1101/672873
Abstract: High-throughput 16S rRNA gene licon sequencing is an essential method for studying the ersity and dynamics of microbial communities. However, this method is presently h ered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases, and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene licon sequence variant (FL-ASV) reference databases that include high-identity references ( .7% identity) for nearly all abundant bacteria ( .01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an ex le. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for licon sequencing, allowing researchers to choose those that are ideal for their ecosystem. The AutoTax taxonomy greatly improves the classification of short-read 16S rRNA gene licon sequence variants (ASVs) at the genus- and species-level, compared to the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.
No related grants have been discovered for Mads Albertsen.