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(2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages.
Cell 185(21), 4023-4037.e18.
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(2022) Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction.
Microbiome 10(1), 183.
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(2022) Population structure of an Antarctic aquatic cyanobacterium.
Microbiome 10(1), 207.
10.1186/s40168-022-01404-x
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(2022) Microbial communities and biogeochemical functioning across peatlands in the Athabasca Oil Sands region of Canada: Implications for reclamation and management.
Land Degradation and Development .
10.1002/ldr.4549
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(2022) Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.
Microbiome 10(1), 5.
10.1186/s40168-021-01194-8
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(2022) Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits.
Microbiome 10(1), 241.
10.1186/s40168-022-01424-7
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(2022) Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-17.
10.1038/s41396-022-01345-1
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(2022) Poisson hurdle model-based method for clustering microbiome features.
Bioinformatics 39(1), btac782.
10.1093/bioinformatics/btac782
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(2022) Exploring the roles of microbes in facilitating plant adaptation to climate change.
Biochemical Journal 479(3), 327-335.
10.1042/bcj20210793
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(2022) Pathway-Centric Analysis of Microbial Metabolic Potential and Expression Along Nutrient and Energy Gradients in the Western Atlantic Ocean.
Frontiers in Marine Science 9, 867310.
10.3389/fmars.2022.867310
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(2022) Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean.
Limnology and Oceanography .
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(2022) Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland.
Microbial Ecology , 1-17.
10.1007/s00248-022-02071-z
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(2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria.
Virus Evolution 8(2), veac070.
10.1093/ve/veac070
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(2022) HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi.
Microbiome 10(1), 199.
10.1186/s40168-022-01391-z
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(2022) Environmental predictors of electroactive bacterioplankton in small boreal lakes.
Environmental Microbiology .
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(2022) Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.
mSystems 7(4), e00516-22.
10.1128/msystems.00516-22
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(2022) Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.
Proceedings of the National Academy of Sciences of the United States of America 119(37), e2200014119.
10.1073/pnas.2200014119
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(2022) Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat.
Environmental Science and Technology 56(20), 14462-14477.
10.1021/acs.est.2c03566
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(2022) Deep-branching acetogens in serpentinized subsurface fluids of Oman.
Proceedings of the National Academy of Sciences of the United States of America 119(42), e2206845119.
10.1073/pnas.2206845119
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(2022) Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils.
Communications Earth & Environment 3(1), 304.
10.1038/s43247-022-00642-z
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(2022) Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe.
Microbiology Resource Announcements 11(10), e00400-22.
10.1128/mra.00400-22
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(2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea.
PLoS Biology 20(1), e3001508.
10.1371/journal.pbio.3001508
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(2022) Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics.
Frontiers in Microbiology 13, 879116.
10.3389/fmicb.2022.879116
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(2022) Metagenomes from Arctic Soil Microbial Communities from the Barrow Environmental Observatory, Utqiaġvik, AK, USA.
Microbiology Resource Announcements 11(8), e00528-22.
10.1128/mra.00528-22
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(2022) Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns.
Genes 13(1), 148.
10.3390/genes13010148
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(2022) Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming.
Global Change Biology .
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(2022) Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages.
mBio 13(3), e00651-22.
10.1128/mbio.00651-22
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(2022) Metagenome-Assembled Genomes for “Candidatus Phormidium sp. Strain AB48” and Co-occurring Microorganisms from an Industrial Photobioreactor Environment.
Microbiology Resource Announcements 11(12), e00447-22.
10.1128/mra.00447-22
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(2022) Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate.
Microbiology Resource Announcements 11(8), e00292-22.
10.1128/mra.00292-22
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(2022) Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery.
Microbiology Resource Announcements 11(8), e00290-22.
10.1128/mra.00290-22
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(2022) Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(7), 1853-1863.
10.1038/s41396-022-01232-9
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(2022) Microtopography Matters: Belowground CH4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns.
Journal of Geophysical Research Biogeosciences 127(8).
10.1029/2022jg006948
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(2022) Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition.
Soil Biology and Biochemistry 168, 108628.
10.1016/j.soilbio.2022.108628
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(2022) Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities.
mSystems 7(4), e01419-21.
10.1128/msystems.01419-21
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(2022) Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes.
Applied and Environmental Microbiology 88(10), e02449-21.
10.1128/aem.02449-21
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(2022) Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.
Nature Communications 13(1), 2389.
10.1038/s41467-022-30049-5
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(2022) Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities.
ISME Communications 2(1), 54.
10.1038/s43705-022-00132-5
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(2022) Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.
Environmental Microbiology .
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(2022) Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments.
ISME Communications 2(1), 86.
10.1038/s43705-022-00175-8
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(2022) Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(2), 309-314.
10.1038/s41396-022-01341-5
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(2022) Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques.
Environmental Science & Technology 56(3), 2021-2032.
10.1021/acs.est.1c06772
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(2022) Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities.
ISME Communications 2(1), 58.
10.1038/s43705-022-00141-4
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(2022) Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.
Microbiome 10(1), 157.
10.1186/s40168-022-01340-w
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(2022) Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems.
mBio 13(1), e03714-21.
10.1128/mbio.03714-21
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(2022) Soil pH influences the structure of virus communities at local and global scales.
Soil Biology and Biochemistry 166, 108569.
10.1016/j.soilbio.2022.108569
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(2022) Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae).
Genome Biology and Evolution 14(6), evac089.
10.1093/gbe/evac089
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(2022) TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.
ISME Communications 2(1), 111.
10.1038/s43705-022-00189-2
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(2022) Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis.
Nature Communications 13(1), 6454.
10.1038/s41467-022-34105-y
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(2022) Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota.
Nature Microbiology 7(4), 556-569.
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(2022) Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria.
Cell Host & Microbe 30(3), 314-328.e11.
10.1016/j.chom.2022.02.001
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(2022) Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(8), 1957-1969.
10.1038/s41396-022-01245-4
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(2022) Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay.
mSystems 7(1), e01270-21.
10.1128/msystems.01270-21
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(2022) Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park.
Microbiology Resource Announcements , e01065-21.
10.1128/mra.01065-21
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(2022) A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.
Frontiers in Microbiology 12, 761869.
10.3389/fmicb.2021.761869
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(2022) Diversity in the soil virosphere: to infinity and beyond?.
Trends in Microbiology .
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(2022) ORT: A workflow linking genome-scale metabolic models with reactive transport codes.
Bioinformatics (Oxford, England) 38(3), 778-784.
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(2022) GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.
Frontiers in Microbiology 12, 787651.
10.3389/fmicb.2021.787651
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(2022) Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids.
Microbiology Resource Announcements , e01151-21.
10.1128/mra.01151-21
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(2022) Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics.
npj Biofilms and Microbiomes 8(1), 7.
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(2022) Weakened resilience of benthic microbial communities in the face of climate change.
ISME Communications 2(1), 21.
10.1038/s43705-022-00104-9
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(2022) Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.
Applied and Environmental Microbiology 88(11), e00226-22.
10.1128/aem.00226-22
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(2022) Trace metal contents of autotrophic flagellates from contrasting open‐ocean ecosystems.
Limnology and Oceanography Letters 7(4), 354-362.
10.1002/lol2.10258
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(2022) Microbes and Climate Change: a Research Prospectus for the Future.
mBio 13(3), e00800-22.
10.1128/mbio.00800-22
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(2022) Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water.
ACS ES&T Water 2(3), 484-494.
10.1021/acsestwater.1c00436
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(2022) Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate.
Microbiology Resource Announcements 11(7), e00293-22.
10.1128/mra.00293-22
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(2022) Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake.
Environmental Microbiology 24(5), 2576-2603.
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(2022) Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake.
Microbiology Resource Announcements 11(7), e00351-22.
10.1128/mra.00351-22
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2021
(2021) Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.
Communications Biology 4(1).
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(2021) Metagenomes, metatranscriptomes, and metagenome-assembled genomes from chesapeake and Delaware bay (USA) water samples.
Microbiology Resource Announcements 10(21).
10.1128/MRA.00262-21
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(2021) Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages.
Microbiome 9(1), 15.
10.1186/s40168-021-01021-0
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(2021) The widespread IS200/605 transposon family encodes diverse programmable RNA-guided endonucleases.
Science 374(6563), 57-65.
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(2021) Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.
mSystems 6(3), e00537-21.
10.1128/mSystems.00537-21
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(2021) Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.
Nature Communications 12.
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(2021) Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts.
ISME Journal .
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(2021) Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom.
Isme Journal , 15.
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(2021) Extreme dimensions — how big (or small) can tailed phages be?.
Nature Reviews Microbiology 19(7), 407.
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(2021) iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.
ISME Communications 1(1), 77.
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(2021) Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-11.
10.1038/s41396-021-01178-4
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(2021) Whole Community Metatranscriptomes and Lipidomes Reveal Diverse Responses Among Antarctic Phytoplankton to Changing Ice Conditions.
Frontiers in Marine Science 8, 14.
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(2021) Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria.
Phytobiomes Journal 5(1), 60-68.
10.1094/PBIOMES-07-20-0051-R
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(2021) Illuminating the Virosphere Through Global Metagenomics.
Annual Review of Biomedical Data Science 4(1), 369-391.
10.1146/annurev-biodatasci-012221-095114
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(2021) Cultivating the bacterial microbiota of populus roots.
mSystems 6(3).
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(2021) 16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments.
Microbiology Resource Announcements 10(27), e00178-21.
10.1128/mra.00178-21
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(2021) Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.
Nature Communications 12(1).
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(2021) Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes.
Frontiers in Microbiology 12, 17.
10.3389/fmicb.2021.598180
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(2021) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community.
mSystems 6(3).
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(2021) DOE JGI metagenome workflow.
mSystems 6(3).
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(2021) Global overview and major challenges of host prediction methods for uncultivated phages.
Current Opinion in Virology 49, 117-126.
10.1016/j.coviro.2021.05.003
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(2021) Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean.
Nature Microbiology 6(2), 173-+.
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(2021) Different threats, same response.
Nature Plants 7(5), 544-545.
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(2021) A global metagenomic map of urban microbiomes and antimicrobial resistance.
Cell 184(13), 3376-3393.e17.
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(2021) Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways.
Nature Communications 12(1).
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(2021) Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern.
Genes 12(10), 1609.
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(2021) Perspective on taxonomic classification of uncultivated viruses.
Current Opinion in Virology 51, 207-215.
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(2021) Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes.
Plant and Soil .
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(2021) 16S rRNA gene amplicon sequencing data from flooded rice paddy mesocosms treated with different silicon-rich soil amendments.
Microbiology Resource Announcements 10(27).
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(2021) Global Diversity and Biogeography of the Zostera marina Mycobiome.
Applied and Environmental Microbiology 87(12), 1-19.
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(2021) Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring.
Applied and Environmental Microbiology 87(23), e01598-21.
10.1128/aem.01598-21
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(2021) Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization.
BMC Bioinformatics 22(1).
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(2021) VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses.
Microbiome 9(1), 13.
10.1186/s40168-020-00990-y
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(2021) Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber.
Isme Journal 15(2), 421-434.
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(2021) Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.
Current Biology 31(7), 1393-1402.e5.
10.1016/j.cub.2021.01.018
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(2021) Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-11.
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(2021) Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential.
Journal of Environmental Management 299.
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(2021) Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.
Microbiome 9(1), 21.
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(2021) Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence of different hardwood tree species.
Soil Biology and Biochemistry 156.
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(2021) Virus-associated organosulfur metabolism in human and environmental systems.
Cell Reports 36(5).
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(2021) Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages.
Nature Communications 12(1).
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(2021) Pangenomics reveals alternative environmental lifestyles among chlamydiae.
Nature Communications 12(1).
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(2021) Peatland microbial community responses to plant functional group and drought are depth-dependent.
Molecular Ecology 30(20), 5119-5136.
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(2021) Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups.
ISME Journal .
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(2021) Methane-derived carbon flows into host–virus networks at different trophic levels in soil.
Proceedings of the National Academy of Sciences 118(32), e2105124118.
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(2021) Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses.
Soil Biology and Biochemistry 160.
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(2021) Mercury methylation by metabolically versatile and cosmopolitan marine bacteria.
Isme Journal , 16.
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(2021) Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.
PLOS Biology 19(11), e3001442.
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(2021) Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis.
Frontiers in Microbiology 11.
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(2021) Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics.
Science 373(6553).
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(2021) The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.
Nature Communications 12(1).
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(2021) Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion.
Plant and Soil , 1-20.
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(2021) New Insights Into the Influence of Plant and Microbial Diversity on Denitrification Rates in a Salt Marsh.
Wetlands 41(2), 14.
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(2021) Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.
Microbiome 9(1).
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(2021) Decrypting bacterial polyphenol metabolism in an anoxic wetland soil.
Nature Communications 12(1).
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(2021) Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-12.
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(2021) Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
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(2021) Genomes OnLine Database (GOLD) v.8: overview and updates.
Nucleic Acids Res 49(D1), D723-D733.
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(2021) Draft Metagenomes of Endolithic Cyanobacteria and Cohabitants from Hyper-Arid Deserts.
Microbiology Resource Announcements 10(30), e00206-21.
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(2021) Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.
Nature Microbiology 6(7), 960-970.
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(2021) Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion.
Mbio 12(1), 12.
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(2021) Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater.
Nature Microbiology 6(4), 524-+.
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(2021) Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms.
ISME Journal .
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(2021) Remarkably coherent population structure for a dominant Antarctic Chlorobium species.
Microbiome 9(1), 231.
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(2021) Virus Bioinformatics.
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(2021) Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.
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(2021) Fungal community response to long-term soil warming with potential implications for soil carbon dynamics.
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(2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.
PLoS One 8(3), e59927.
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(2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions.
Proc Natl Acad Sci U S A 110(16), 6548-53.
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(2013) Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill.
ISME J .
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(2013) Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.
Appl Environ Microbiol 79(9), 2932-43.
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(2013) Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.
PLoS One 8(9), e73827.
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(2013) Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications.
PLoS Genet 9(1).
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2012
(2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.
ISME J 6(9), 1688-701.
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(2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill.
Environ Microbiol 14(9), 2405-16.
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(2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
Environ Microbiol 14(1), 207-27.
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(2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community.
ISME J 6(9), 1702-14.
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(2012) Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay.
ISME J 6(4), 863-74.
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(2012) Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia.
MBio 3(1).
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(2012) Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide.
Environ Microbiol 14(5), 1145-58.
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(2012) Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris).
Microb Ecol 63(4), 719-25.
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(2012) Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia.
Biotechnol Bioeng 109(5), 1140-5.
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(2012) Differences in crop bacterial community structure between hoatzins from different geographical locations.
Research in Microbiology 163(3), 211-220.
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(2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.
ISME J 6(3), 531-41.
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(2012) Microbes in thawing permafrost: the unknown variable in the climate change equation.
ISME J 6(4), 709-12.
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(2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria.
Appl Environ Microbiol 78(3), 752-8.
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(2012) Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion.
PLoS One 7(6), e39689.
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(2012) A framework for human microbiome research.
Nature 486(7402), 215-21.
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(2012) Structure, function and diversity of the healthy human microbiome.
Nature 486(7402), 207-14.
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(2012) Unlocking the potential of metagenomics through replicated experimental design.
Nature Biotechnology 30(6), 513-520.
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(2012) Defining the core Arabidopsis thaliana root microbiome.
Nature 488(7409), 86-90.
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(2012) Individual genome assembly from complex community short-read metagenomic datasets.
ISME J 6(4), 898-901.
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(2012) Individual genome assembly from complex community short-read metagenomic datasets.
ISME J 6(4), 898-901.
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(2012) IMG/M: the integrated metagenome data management and comparative analysis system.
Nucleic Acids Res 40(Database issue), D123-9.
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(2012) IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.
PLoS One 7(7), e40151.
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(2012) Effect of oxygen minimum zone formation on communities of marine protists.
ISME J 6(8), 1586-601.
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(2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.
Proc Natl Acad Sci U S A 109(33), 13272-7.
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(2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis.
Curr Opin Biotechnol 23(1), 9-15.
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(2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis.
Molecular Plant-Microbe Interactions 25(1), 28-36.
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(2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis.
Molecular Plant-Microbe Interactions 25(1), 28-36.
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(2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study.
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(2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem.
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(2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips.
PLoS One 7(5), e36740.
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(2012) Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis.
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(2012) Global distribution of a wild alga revealed by targeted metagenomics.
Curr Biol 22(17), R675-7.
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2011
(2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio.
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(2011) Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome.
Isme Journal 5(1), 161-164.
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(2011) Genomics for key players in the N cycle from guinea pigs to the next frontier.
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(2011) Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil.
Plos One 6(4).
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(2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard.
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(2011) Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass.
Applied and Environmental Microbiology 77(16), 5804-5812.
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(2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Science 331(6016), 463-7.
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(2011) Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.
J Allergy Clin Immunol 127(2), 372-381 e1-3.
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(2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium.
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(2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.
Nature 480(7377), 368-71.
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(2011) ClaMS: A Classifier for Metagenomic Sequences.
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(2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies.
Science 333(6042), 646-8.
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(2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction.
Biotechnol Bioeng 108(9), 2088-98.
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(2011) Phage encoded H-NS: a potential achilles heel in the bacterial defence system.
PLoS One 6(5), e20095.
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(2011) Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean.
Science 333(6047), 1296-1300.
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(2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
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2010
(2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community.
PLoS One 5(1), e8812.
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(2010) Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
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(2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil.
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(2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.
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(2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities.
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(2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.
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2008
(2008) Identification of ancient remains through genomic sequencing.
Genome Research 18(8), 1347-1353.
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(2008) Annotation of metagenome short reads using proxygenes.
Bioinformatics 24(16), I7-I13.
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(2008) Toward a standards-compliant genomic and metagenomic publication record.
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(2008) Microbiology - Metagenomics.
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(2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal.
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(2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
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(2008) Assembly of viral metagenomes from yellowstone hot springs.
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(2008) A renaissance for the pioneering 16S rRNA gene.
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(2008) The airborne metagenome in an indoor urban environment.
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(2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.
Isme Journal 2(11), 1146-1156.
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2006
(2006) An experimental metagenome data management and analysis system.
Bioinformatics 22(14), e359-67.
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Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface.
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Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs).
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The endosymbiotic box of protective tricks.
Nature Reviews Microbiology 20(5), 255-255.
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Small partners, big impacts.
Nature Reviews Microbiology 20(3), 127-127.
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