ORCID Profile
0000-0001-6479-8427
Current Organisations
E O Lawrence Berkeley National Laboratory
,
DOE Joint Genome Institute
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Publications
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.
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Publisher: Springer Science and Business Media LLC
Date: 17-12-2019
DOI: 10.1038/NBT.4306
Identification of beneficial and detrimental bacteria that impact sorghum responses to drought using multi-scale and multi-system microbiome comparisons
Publisher: Cold Spring Harbor Laboratory
Date: 14-04-2021
DOI: 10.1101/2021.04.13.437608
Abstract: Drought is a major abiotic stress that limits agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome ersity in the root and rhizosphere and may lead to enrichment of specific groups of microbes, such as Actinobacteria . How these changes ultimately affect plant health is not well understood. In parallel, model systems have been used to tease apart the specific interactions between plants and single, or small groups of microbes. However, translating this work into crop species and achieving increased crop yields within noisy field settings remains a challenge. Thus, the next scientific leap forward in microbiome research must cross the great lab-to-field ide. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key beneficial and detrimental, root associated microbes that robustly affect drought stressed plant phenotypes. Fifty-three bacterial strains, originally characterized for association with Arabidopsis , were applied to sorghum seeds and their effect on root growth was monitored for seven days. Two Arthrobacter strains, members of the Actinobacteria phylum, caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, strains of Variovorax were able to protect both Arabidopsis and sorghum from the RGI caused by Arthrobacter . As a transitional system, we tested the synthetic communities through a 24-day high-throughput sorghum phenotyping assay and found that during drought stress, plants colonized by Arthrobacter were significantly smaller and had reduced leaf water content as compared to control plants. However, plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across well-watered and drought conditions. Drought responsive microbes were identified, including an enrichment in Actinobacteria , consistent with previous findings. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a newly developed method and were then able to observe that the abundance of Arthrobacter strains negatively correlated with plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of high confidence bacterial taxa that positively associated with plant growth under drought stress. A three-tiered experimental system connected reductionist and ecological approaches and identified beneficial and deleterious bacterial strains for sorghum under drought stress.
Defining the core Arabidopsis thaliana root microbiome
Publisher: Springer Science and Business Media LLC
Date: 08-2012
DOI: 10.1038/NATURE11237
A genomic catalog of Earth’s microbiomes
Publisher: Springer Science and Business Media LLC
Date: 09-11-2020
DOI: 10.1038/S41587-020-0718-6
Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to ,000 metagenomes collected from erse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic ersity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Plant–microbiome interactions: from community assembly to plant health
Publisher: Springer Science and Business Media LLC
Date: 12-08-2020
The Enduring Legacy of Small Subunit rRNA in Microbiology
Publisher: Wiley
Date: 03-05-2011
Author Correction: A genomic catalog of Earth’s microbiomes
Publisher: Springer Science and Business Media LLC
Date: 04-2021
DOI: 10.1038/S41587-021-00898-4
Abstract: A Correction to this paper has been published: 0.1038/s41587-021-00898-4.
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
Publisher: Springer Science and Business Media LLC
Date: 05-08-2010
Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
Publisher: Springer Science and Business Media LLC
Date: 06-05-2022
DOI: 10.1038/S41396-022-01245-4
Abstract: Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome ersity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis -associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter -caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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.
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
Publisher: Cold Spring Harbor Laboratory
Date: 17-01-2020
DOI: 10.1101/2020.01.16.907998
Abstract: The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass s les incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
Erratum: Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea
Publisher: Springer Science and Business Media LLC
Date: 22-07-2014
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
Publisher: Springer Science and Business Media LLC
Date: 14-09-2020
DOI: 10.1038/S41396-020-00769-X
Abstract: The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass s les incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
Publisher: Wiley
Date: 17-10-2011
DOI: 10.1111/J.1462-2920.2011.02593.X
Abstract: Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of ersity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.
Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Publisher: Frontiers Media SA
Date: 25-02-2016
Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum
Publisher: Cold Spring Harbor Laboratory
Date: 09-02-2023
DOI: 10.1101/2023.02.08.527764
Abstract: Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 erse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly influenced the root-associated bacterial communities and root metabolite composition of sorghum. Sorghum NUE was positively correlated with the bacterial richness and ersity in the rhizosphere. The greater alpha ersity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas . Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to N stress and indicate that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our study provides new insight into the links between host genetic regulation of root metabolites and root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
High-resolution phylogenetic microbial community profiling
Publisher: Springer Science and Business Media LLC
Date: 09-02-2016
Poisson hurdle model-based method for clustering microbiome features
Publisher: Oxford University Press (OUP)
Date: 05-12-2022
DOI: 10.1093/BIOINFORMATICS/BTAC782
Abstract: High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. R package is freely available for download at ackage=PHclust. Supplementary data are available at Bioinformatics online.
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.
Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal
Publisher: Springer Science and Business Media LLC
Date: 25-07-2013
‘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.
Author Correction: Plant–microbiome interactions: from community assembly to plant health
Publisher: Springer Science and Business Media LLC
Date: 23-11-2020
High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake
Publisher: Proceedings of the National Academy of Sciences
Date: 30-09-2013
Abstract: Horizontal gene exchange across species boundaries is considered infrequent relative to vertical inheritance that maintains species coherence. However, haloarchaea living in hypersaline environments take a more relaxed approach to gene exchange. Here we demonstrate that in Deep Lake, Antarctica, haloarchaea exchange DNA between distinct genera, not just species, with some of the DNA being long (up to 35 kb) and virtually 100% conserved. With extremely low cell ision rates in the cold (e.g., six generations per year), the remarkable extent of lateral exchange could conceivably homogenize the population. It is therefore equally notable that despite the demonstrated capacity for exchange, different genera are maintained, their coexistence being linked to genomic differences conferring ecotype distinctions that enable niche adaptation.
Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots
Publisher: American Society for Microbiology
Date: 12-09-2019
DOI: 10.1128/MRA.00432-19
Abstract: Agrobacterium sp. strain 33MFTa1.1 was isolated for functional host-microbe interaction studies from the Thlaspi arvense root-associated microbiome. The complete genome is comprised of a circular chromosome of 2,771,937 bp, a linear chromosome of 2,068,443 bp, and a plasmid of 496,948 bp, with G+C contents of 59%, 59%, and 58%, respectively.
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.
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
Publisher: Springer Science and Business Media LLC
Date: 23-01-2015
Erratum: California voters and CIRM—will lightning strike twice?
Publisher: Springer Science and Business Media LLC
Date: 06-07-2018
DOI: 10.1038/NBT0718-660D
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
Publisher: Springer Science and Business Media LLC
Date: 08-2014
Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea
Publisher: Springer Science and Business Media LLC
Date: 20-02-2014
A call for standardized classification of metagenome projects
Publisher: Wiley
Date: 07-2010
Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide
Publisher: Informa UK Limited
Date: 04-11-2019
Correction: Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
Publisher: Springer Science and Business Media LLC
Date: 15-06-2023
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Publisher: Public Library of Science (PLoS)
Date: 19-07-2013
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.
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.
Publisher Correction: A genomic catalog of Earth’s microbiomes
Publisher: Springer Science and Business Media LLC
Date: 18-11-2020
DOI: 10.1038/S41587-020-00769-4
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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.
Related Organisations
E O Lawrence Berkeley National Laboratory
Location: United States of America
Related Funding Activities
No related grants have been discovered for Susannah Tringe.