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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Metagenome Publications

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2022

Acinas, Silvia G. et al. (2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185(21), 4023-4037.e18. 10.1016/j.cell.2022.08.023
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Adams, Paul D. et al. (2022) Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome 10(1), 183. 10.1186/s40168-022-01377-x
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Allen, Michelle A. et al. (2022) Population structure of an Antarctic aquatic cyanobacterium. Microbiome 10(1), 207. 10.1186/s40168-022-01404-x
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Allingham, Shaun M et al. (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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Amundson, Kaela K. et al. (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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Anantharaman, Karthik et al. (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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Arruda, Paulo et al. (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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Barnes, Elle et al. (2022) Poisson hurdle model-based method for clustering microbiome features. Bioinformatics 39(1), btac782. 10.1093/bioinformatics/btac782
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Barnes, Elle M. et al. (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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Bhatia, Maya P. et al. (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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Bhatia, Maya P. et al. (2022) Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean. Limnology and Oceanography . 10.1002/lno.12275
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Birnbaum, Christina et al. (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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Bischoff, Vera et al. (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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Blazewicz, Steven J. et al. (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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Bond, Daniel R. et al. (2022) Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environmental Microbiology . 10.1111/1462-2920.16314
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Borton, Mikayla A. et al. (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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Bosak, Tanja et al. (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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Bosworth, Lily B. et al. (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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Boyd, Eric S. et al. (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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Brambilla, Diego et al. (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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Carper, Dana L. et al. (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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Chadwick, Grayson L. et al. (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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Cooper, Zachary S. et al. (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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Dafflon, Baptiste et al. (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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Danielson, Rachel E. et al. (2022) . 175, 179-258. 10.1016/bs.agron.2022.04.001
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de Mesquita, Clifton P. Bueno et al. (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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DeAngelis, Kristen M. et al. (2022) Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming. Global Change Biology . 10.1111/gcb.16544
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Demina, Tatiana A. et al. (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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Dofher, Kalen et al. (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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Donohue, Timothy J. et al. (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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Donohue, Timothy J. et al. (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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Dove, Nicholas C. et al. (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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Ernakovich, Jessica G. et al. (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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Fiore-Donno, Anna Maria et al. (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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Fisher, Kirsten et al. (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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Gagliano, Maria Cristina et al. (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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Gao, Shaoming et al. (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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Gilbert, Naomi E. et al. (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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Gronniger, Jessica L. et al. (2022) Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables. Environmental Microbiology . 10.1111/1462-2920.16086
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Hatzenpichler, Roland et al. (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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Hazard, Christina et al. (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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Honeker, Linnea K. et al. (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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Hug, Laura A. et al. (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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Hwang, Chung Yeon et al. (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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Kolton, Max et al. (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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Lee, Sungeun et al. (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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Li, Yuanning et al. (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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McDaniel, E. A. et al. (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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Michael Beman, J. et al. (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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Ostrowski, Matthew P. et al. (2022) Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nature Microbiology 7(4), 556-569. 10.1038/s41564-022-01093-0
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Pudlo, Nicholas A. et al. (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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Qi, Mingsheng et al. (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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Rasmussen, Anna N. et al. (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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Reichart, Nicholas J. et al. (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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Rodríguez-Gijón, Alejandro et al. (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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Roux, Simon et al. (2022) Diversity in the soil virosphere: to infinity and beyond?. Trends in Microbiology . 10.1016/j.tim.2022.05.003
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Rubinstein, Rebecca L. et al. (2022) ORT: A workflow linking genome-scale metabolic models with reactive transport codes. Bioinformatics (Oxford, England) 38(3), 778-784. 10.1093/bioinformatics/btab753
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Ruhl, Ilona A. et al. (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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Scarborough, Matthew J. et al. (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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Schweitzer, Hannah D. et al. (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. 10.1038/s41522-022-00267-2
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Seidel, Laura et al. (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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Seitz, Valerie A. et al. (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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Sofen, Laura E. et al. (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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Tiedje, James M. et al. (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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Van Houghton, Brett D. et al. (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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Walters, Kevin A. et al. (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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Williams, Timothy J. et al. (2022) Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake. Environmental Microbiology 24(5), 2576-2603. 10.1111/1462-2920.16026
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Zepernick, Brittany N. et al. (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

Acinas, S. G. et al. (2021) Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology 4(1). 10.1038/s42003-021-02112-2
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Ahmed, M. A. et al. (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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Albanese, D. et al. (2021) Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. Microbiome 9(1), 15. 10.1186/s40168-021-01021-0
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Altae-Tran, Han et al. (2021) The widespread IS200/605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374(6563), 57-65. 10.1126/science.abj6856
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Ankita Kothari et al. (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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Avila-Magaña, Viridiana et al. (2021) Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nature Communications 12. 10.1038/s41467-021-25950-4
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Bachy, C. et al. (2021) Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. ISME Journal . 10.1038/s41396-021-00989-9
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Ben Francis, T. et al. (2021) Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. Isme Journal , 15. 10.1038/s41396-021-00928-8
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Berg, M. et al. (2021) Extreme dimensions — how big (or small) can tailed phages be?. Nature Reviews Microbiology 19(7), 407. 10.1038/s41579-021-00574-z
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Bolduc, Benjamin et al. (2021) iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Communications 1(1), 77. 10.1038/s43705-021-00083-3
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Bowers, Robert M. et al. (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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Bowman, J. S. et al. (2021) Whole Community Metatranscriptomes and Lipidomes Reveal Diverse Responses Among Antarctic Phytoplankton to Changing Ice Conditions. Frontiers in Marine Science 8, 14. 10.3389/fmars.2021.593566
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Bowsher, A. W. et al. (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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Call, L. et al. (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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Carper, D. L. et al. (2021) Cultivating the bacterial microbiota of populus roots. mSystems 6(3). 10.1128/mSystems.01306-20
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Chan, Clara S. et al. (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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Chen, Y. et al. (2021) Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nature Communications 12(1). 10.1038/s41467-021-25678-1
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Chiniquy, D. et al. (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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Chuckran, P. F. et al. (2021) Rapid response of nitrogen cycling gene transcription to labile carbon amendments in a soil microbial community. mSystems 6(3). 10.1128/mSystems.00161-21
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Clum, A. et al. (2021) DOE JGI metagenome workflow. mSystems 6(3). 10.1128/MSYSTEMS.00804-20
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Coclet, C. et al. (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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Cohen, N. R. et al. (2021) Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nature Microbiology 6(2), 173-+. 10.1038/s41564-020-00814-7
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Cole, B. J. et al. (2021) Different threats, same response. Nature Plants 7(5), 544-545. 10.1038/s41477-021-00915-z
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Danko, D. et al. (2021) A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184(13), 3376-3393.e17. 10.1016/j.cell.2021.05.002
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De Anda, V. et al. (2021) Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nature Communications 12(1). 10.1038/s41467-021-22736-6
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de Mesquita, Clifton P. Bueno et al. (2021) Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes 12(10), 1609. 10.3390/genes12101609
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Dutilh, Bas E. et al. (2021) Perspective on taxonomic classification of uncultivated viruses. Current Opinion in Virology 51, 207-215. 10.1016/j.coviro.2021.10.011
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Dykes, G. E. et al. (2021) Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes. Plant and Soil . 10.1007/s11104-021-05103-8
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Dykes, G. E. et al. (2021) 16S rRNA gene amplicon sequencing data from flooded rice paddy mesocosms treated with different silicon-rich soil amendments. Microbiology Resource Announcements 10(27). 10.1128/MRA.00178-21
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Ettinger, C. L. et al. (2021) Global Diversity and Biogeography of the Zostera marina Mycobiome. Applied and Environmental Microbiology 87(12), 1-19. 10.1128/AEM.02795-20
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Fernandes-Martins, Maria C. et al. (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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Khan, M. A. W. et al. (2019) Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol Ecol 95(2). 10.1093/femsec/fiy230
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Ladau, J. et al. (2019) Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology. Trends Microbiol . 10.1016/j.tim.2019.03.003
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Li, Q. et al. (2019) Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance. Appl Environ Microbiol . 10.1128/AEM.02931-18
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Malmstrom, R. R. et al. (2019) Advancing Genome-Resolved Metagenomics beyond the Shotgun. mSystems 4(3). 10.1128/mSystems.00118-19
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Mao, X. et al. (2019) Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor. Water Res 158, 146-156. 10.1016/j.watres.2019.04.038
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Marotz, C. et al. (2019) Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary. Biotechniques . 10.2144/btn-2018-0192
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Martinez, M. A. et al. (2019) Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol 42(1), 54-66. 10.1016/j.syapm.2018.12.003
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Mizuno, C. M. et al. (2019) Numerous cultivated and uncultivated viruses encode ribosomal proteins. Nat Commun 10(1), 752. 10.1038/s41467-019-08672-6
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Nayfach, S. et al. (2019) Novel insights from uncultivated genomes of the global human gut microbiome. Nature . 10.1038/s41586-019-1058-x
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Nowinski, B. et al. (2019) Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Sci Data 6(1), 129. 10.1038/s41597-019-0132-4
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Paez-Espino, D. et al. (2019) Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 7(1), 157. 10.1186/s40168-019-0768-5
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Roux, S. et al. (2019) Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol 4(11), 1895-1906. 10.1038/s41564-019-0510-x
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Roux, S. et al. (2019) A Viral Ecogenomics Framework To Uncover the Secrets of Nature's "Microbe Whisperers". mSystems 4(3). 10.1128/mSystems.00111-19
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Roux, S. et al. (2019) Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ 7, e6902. 10.7717/peerj.6902
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Sevim, V. et al. (2019) Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 6(1), 285. 10.1038/s41597-019-0287-z
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Sheflin, A. M. et al. (2019) Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis. Plant Direct 3(3), e00122. 10.1002/pld3.122
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Shi, L. et al. (2019) SpaRC: scalable sequence clustering using Apache Spark. Bioinformatics 35(5), 760-768. 10.1093/bioinformatics/bty733
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Sieber, C. M. K. et al. (2019) Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. MBio 10(6). 10.1128/mBio.02128-19
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St John, E. et al. (2019) Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota. Environ Microbiol Rep 11(2), 262-270. 10.1111/1758-2229.12740
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Trubl, G. et al. (2019) Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ 7, e7265. 10.7717/peerj.7265
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Vigneron, A. et al. (2019) Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments. mSystems 4(1). 10.1128/mSystems.00091-18
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Wang, B. et al. (2019) Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. ISME J 13(12), 3067-3079. 10.1038/s41396-019-0493-x
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Youssef, N. H. et al. (2019) Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl Environ Microbiol 85(10). 10.1128/AEM.00110-19
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Zheng, H. et al. (2019) Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 116(51), 25909-25916. 10.1073/pnas.1916224116
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2018

Anantharaman, K. et al. (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J . 10.1038/s41396-018-0078-0
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Beller, H. R. et al. (2018) Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nat Chem Biol . 10.1038/s41589-018-0017-4
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Borton, M. A. et al. (2018) Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proc Natl Acad Sci U S A 115(28), E6585-E6594. 10.1073/pnas.1800155115
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Borton, Mikayla A. et al. (2018) Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale. Environmental Microbiology 20(12), 4596-4611. 10.1111/1462-2920.14467
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Crits-Christoph, A. et al. (2018) Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558(7710), 440-444. 10.1038/s41586-018-0207-y
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Espinola, F. et al. (2018) Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb Ecol 75(1), 123-139. 10.1007/s00248-017-1028-5
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Hausmann, B. et al. (2018) Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J . 10.1038/s41396-018-0077-1
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Khdhiri, M. et al. (2018) Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H-2-oxidation activity measured in three soils exposed to H-2. Soil Biology & Biochemistry 125, 239-243. 10.1016/j.soilbio.2018.07.020
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Kroeger, M. E. et al. (2018) New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. Front Microbiol 9, 1635. 10.3389/fmicb.2018.01635
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Levy, A. et al. (2018) Genomic features of bacterial adaptation to plants. Nat Genet 50(1), 138-150. 10.1038/s41588-017-0012-9
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Lin, H. et al. (2018) Combining Hadoop with MPI to Solve Metagenomics Problems that are both Data- and Compute-intensive. International Journal of Parallel Programming 46(4), 762-775. 10.1007/s10766-017-0524-z
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Mackelprang, R. et al. (2018) Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Front Microbiol 9, 1775. 10.3389/fmicb.2018.01775
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Nash, M. V. et al. (2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol . 10.1093/femsec/fiy114
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Probst, A. J. et al. (2018) Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat Microbiol 3(3), 328-336. 10.1038/s41564-017-0098-y
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Roux, S. et al. (2018) A viral reckoning: viruses emerge as essential manipulators of global ecosystems. Environ Microbiol Rep . 10.1111/1758-2229.12700
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Roux, Simon et al. (2018) Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology 37, 29. 10.1038/nbt.4306 https://www.nature.com/articles/nbt.4306#supplementary-information
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Schulz, F. et al. (2018) Hidden diversity of soil giant viruses. Nature Communications 9, 9. 10.1038/s41467-018-07335-2
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Sieber, C. M. K. et al. (2018) Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3(7), 836-843. 10.1038/s41564-018-0171-1
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Smith, G. J. et al. (2018) Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. MBio 9(6). 10.1128/mBio.00815-18
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Stough, J. M. A. et al. (2018) Diversity of Active Viral Infections within the Sphagnum Microbiome. Appl Environ Microbiol 84(23). 10.1128/AEM.01124-18
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Tas, N. et al. (2018) Landscape topography structures the soil microbiome in arctic polygonal tundra. Nat Commun 9(1), 777. 10.1038/s41467-018-03089-z
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Trubl, G. et al. (2018) Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. Msystems 3(5), 21. 10.1128/mSystems.00076-18
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Walters, W. A. et al. (2018) Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci U S A 115(28), 7368-7373. 10.1073/pnas.1800918115
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Wyman, S. K. et al. (2018) A most wanted list of conserved microbial protein families with no known domains. Plos One 13(10). 10.1371/journal.pone.0205749
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Yao, Q. et al. (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2(3), 499-509. 10.1038/s41559-017-0463-5
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Yao, Q. et al. (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2(3), 499-509. 10.1038/s41559-017-0463-5
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2017

Becraft, E. D. et al. (2017) Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 8, 2264. 10.3389/fmicb.2017.02264
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Booker, A. E. et al. (2017) Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales. mSphere 2(4). 10.1128/mSphereDirect.00257-17
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Chen, I. A. et al. (2017) IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 45(D1), D507-D516. 10.1093/nar/gkw929
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Chen, L. X. et al. (2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J . 10.1038/s41396-017-0002-z
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D'Haeseleer, P. et al. (2017) Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Stand Genomic Sci 12, 67. 10.1186/s40793-017-0279-6
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Fernandez-Gonzalez, A. J. et al. (2017) The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils. Sci Rep 7(1), 6008. 10.1038/s41598-017-06112-3
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Gontang, E. A. et al. (2017) Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PLoS One 12(5), e0177189. 10.1371/journal.pone.0177189
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Hamilton, J. J. et al. (2017) Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. mSystems 2(4). 10.1128/mSystems.00091-17
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Hawley, A. K. et al. (2017) A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 4, 170160. 10.1038/sdata.2017.160
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Hawley, A. K. et al. (2017) Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun 8(1), 1507. 10.1038/s41467-017-01376-9
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He, S. et al. (2017) Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2(5). 10.1128/mSphere.00277-17
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Hu, P. et al. (2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A 114(28), 7432-7437. 10.1073/pnas.1703424114
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Hu, P. et al. (2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. Proc Natl Acad Sci U S A . 10.1073/pnas.1703424114
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Jennings, R. M. et al. (2017) Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities. Front Microbiol 8, 88. 10.3389/fmicb.2017.00088
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Jungbluth, S. P. et al. (2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ 5, e3134. 10.7717/peerj.3134
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Jungbluth, S. P. et al. (2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ 5, e3134. 10.7717/peerj.3134
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Kamke, J. et al. (2017) Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. BMC Res Notes 10(1), 367. 10.1186/s13104-017-2671-0
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Kantor, R. S. et al. (2017) Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. Environ Sci Technol 51(5), 2944-2953. 10.1021/acs.est.6b04477
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Khdhiri, M. et al. (2017) The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil. Appl Environ Microbiol 83(11). 10.1128/AEM.00275-17
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Lamit, L. J. et al. (2017) Patterns and drivers of fungal community depth stratification in Sphagnum peat. FEMS Microbiol Ecol 93(7). 10.1093/femsec/fix082
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Li, H. et al. (2017) Lignocellulose pretreatment in a fungus-cultivating termite. Proc Natl Acad Sci U S A 114(18), 4709-4714. 10.1073/pnas.1618360114
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Li, H. et al. (2017) Lignocellulose pretreatment in a fungus-cultivating termite. Proc Natl Acad Sci U S A 114(18), 4709-4714. 10.1073/pnas.1618360114
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Men, Y. et al. (2017) Metagenomic and metatranscriptomic analyses reveal structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoid-providing microorganisms under cobalamin-limited condition. Appl Environ Microbiol . 10.1128/AEM.03508-16
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Meyer, K. M. et al. (2017) Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Mol Ecol 26(6), 1547-1556. 10.1111/mec.14011
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Olm, M. R. et al. (2017) The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. MBio 8(1). 10.1128/mBio.01969-16
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Roux, S. et al. (2017) Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat Commun 8(1), 858. 10.1038/s41467-017-01086-2
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Schulz, F. et al. (2017) Giant viruses with an expanded complement of translation system components. Science 356(6333), 82-85. 10.1126/science.aal4657
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Staley, C. et al. (2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome 5(1), 65. 10.1186/s40168-017-0287-1
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Staley, C. et al. (2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism. Microbiome 5(1), 65. 10.1186/s40168-017-0287-1
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Theodosiou, T. et al. (2017) NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. BMC Res Notes 10(1), 278. 10.1186/s13104-017-2607-8
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Vigneron, A. et al. (2017) Succession in the petroleum reservoir microbiome through an oil field production lifecycle. ISME J . 10.1038/ismej.2017.78
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Vigneron, A. et al. (2017) Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. Sci Rep 7(1), 16015. 10.1038/s41598-017-16375-5
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Vigneron, A. et al. (2017) Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. Sci Rep 7(1), 16015. 10.1038/s41598-017-16375-5
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Yu, F. B. et al. (2017) Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples. Elife 6. 10.7554/eLife.26580
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Ziels, R.M. et al. (2017) DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies. ISME J , 112-123. 10.1038/ismej.2017.143
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2016

Beall, B. F. et al. (2016) Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate. Environ Microbiol 18(6), 1704-19. 10.1111/1462-2920.12819
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Beam, J. P. et al. (2016) Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs. Frontiers in Microbiology 7, 25. 10.3389/fmicb.2016.00025
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Bendall, M. L. et al. (2016) Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J . 10.1038/ismej.2015.241
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Brown, C. T. et al. (2016) Measurement of bacterial replication rates in microbial communities. Nat Biotechnol 34(12), 1256-1263. 10.1038/nbt.3704
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Daly, R. A. et al. (2016) Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol 1, 16146. 10.1038/nmicrobiol.2016.146
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Denef, V. J. et al. (2016) Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria. Front Microbiol 7, 606. 10.3389/fmicb.2016.00606
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Denef, V. J. et al. (2016) Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation. Appl Environ Microbiol 82(5), 1423-32. 10.1128/AEM.03014-15
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Duncan, D. S. et al. (2016) Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods. Soil Biology & Biochemistry 96, 160-168. 10.1016/j.soilbio.2016.02.002
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Eloe-Fadrosh, E. A. et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun 7, 10476. 10.1038/ncomms10476
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Eloe-Fadrosh, Emiley A. et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nature Microbiology , 15032. 10.1038/nmicrobiol.2015.32
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Fonseca-Garcia, C. et al. (2016) The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity. Frontiers in Microbiology 7, 150. 10.3389/fmicb.2016.00150
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Guibert, L. M. et al. (2016) Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments. Microb Ecol 71(1), 100-12. 10.1007/s00248-015-0698-0
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Hausmann, B. et al. (2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J 10(10), 2365-75. 10.1038/ismej.2016.42
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Hausmann, B. et al. (2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J . 10.1038/ismej.2016.42
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Ikeda-Ohtsubo, W. et al. (2016) 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environ Microbiol . 10.1111/1462-2920.13234
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Jay, Z. J. et al. (2016) The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park. Environ Microbiol 18(12), 4755-4769. 10.1111/1462-2920.13366
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Kamke, J. et al. (2016) Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4(1), 56. 10.1186/s40168-016-0201-2
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Kyrpides, N. C. et al. (2016) Microbiome Data Science: Understanding Our Microbial Planet. Trends Microbiol 24(6), 425-7. 10.1016/j.tim.2016.02.011
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Mosier, A. C. et al. (2016) Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. Frontiers in Microbiology 7, 238. 10.3389/fmicb.2016.00238
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Mukai, T. et al. (2016) Transfer RNAs with novel cloverleaf structures. Nucleic Acids Res . 10.1093/nar/gkw898
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Mukai, T. et al. (2016) Facile Recoding of Selenocysteine in Nature. Angew Chem Int Ed Engl 55(17), 5337-41. 10.1002/anie.201511657
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Paez-Espino, D. et al. (2016) Uncovering Earth's virome. Nature . 10.1038/nature19094
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Piche-Choquette, S. et al. (2016) H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups. PeerJ 4, e1782. 10.7717/peerj.1782
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Rivers, A. R. et al. (2016) Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. Front Microbiol 7, 380. 10.3389/fmicb.2016.00380
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Small, G. E. et al. (2016) Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes. Biogeochemistry 128(3), 353-368. 10.1007/s10533-016-0212-x
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Vavourakis, C. D. et al. (2016) Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Frontiers in Microbiology 7, 211. 10.3389/fmicb.2016.00211
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Vigneron, A. et al. (2016) Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility. Appl Environ Microbiol . 10.1128/AEM.03842-15
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Wagner, M. R. et al. (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 7, 12151. 10.1038/ncomms12151
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Zargar, K. et al. (2016) In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community. Sci Rep 6, 31362. 10.1038/srep31362
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2015

Abdul Rahman, N. et al. (2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome 3, 5. 10.1186/s40168-015-0067-8
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Beam, J.P. et al. (2015) Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. ISME J 10(1), 210-24. 10.1038/ismej.2015.83
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Brown, C. T. et al. (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523(7559), 208-11. 10.1038/nature14486
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Cantor, M. et al. (2015) Elviz - exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics 16, 130. 10.1186/s12859-015-0566-4
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Castelle, C. J. et al. (2015) Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol 25(6), 690-701. 10.1016/j.cub.2015.01.014
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Checcucci, A. et al. (2015) The integrated microbial genome resource of analysis. Methods Mol Biol 1231, 289-95. 10.1007/978-1-4939-1720-4_18
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Gilbert, D. et al. (2015) The Joint Genome Institute Offers Resources Beyond a Core Facility. Microbe 10(7), 289-293. 10.1128/microbe.10.289.1
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Hadjithomas, M. et al. (2015) IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. MBio 6(4). 10.1128/mBio.00932-15
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He, S. et al. (2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio 6(3), e00066-15. 10.1128/mBio.00066-15
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He, S. et al. (2015) Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio 6(3), e00066-15. 10.1128/mBio.00066-15
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Hemme, C. L. et al. (2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 6, 1205. 10.3389/fmicb.2015.01205
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Hudson, C. M. et al. (2015) Lignin-modifying processes in the rhizosphere of arid land grasses. Environ Microbiol 17(12), 4965-78. 10.1111/1462-2920.13020
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Hug, L. A. et al. (2015) Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J . 10.1038/ismej.2015.2
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Hug, L. A. et al. (2015) Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environ Microbiol . 10.1111/1462-2920.12930
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Inskeep, W. P. et al. (2015) Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function. Front Microbiol 6, 1044. 10.3389/fmicb.2015.01044
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Kang, D. D. et al. (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165. 10.7717/peerj.1165
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Kantor, R. S. et al. (2015) Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol . 10.1111/1462-2920.12936
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Kemp, D. W. et al. (2015) Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata. PLoS One 10(12), e0143790. 10.1371/journal.pone.0143790
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Luef, B. et al. (2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6, 6372. 10.1038/ncomms7372
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Markowitz, V. M. et al. (2015) Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System. Trends Microbiol 23(11), 730-41. 10.1016/j.tim.2015.07.012
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Oulas, A. et al. (2015) Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environ Microbiol . 10.1111/1462-2920.13095
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Oyserman, B. O. et al. (2015) Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis. ISME J . 10.1038/ismej.2015.155
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Pernice, M. C. et al. (2015) Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME J . 10.1038/ismej.2015.170
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Piao, H. et al. (2015) Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Front Microbiol 6, 809. 10.3389/fmicb.2015.00809
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Salazar, G. et al. (2015) Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol . 10.1111/mec.13419
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Salazar, G. et al. (2015) Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME J . 10.1038/ismej.2015.137
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Sharon, I. et al. (2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 25(4), 534-43. 10.1101/gr.183012.114
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Shi, L., et al. (2015) Performance evaluation and tuning of BioPig for genomic analysis. Proceedings of the 2015 International Workshop on Data-Intensive Scalable Computing Systems , 1-7. 10.1145/2831244.2831252
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Singer, E. et al. (2015) Similar Microbial Communities Found on Two Distant Seafloor Basalts. Frontiers in Microbiology 6. ARTN 1409 10.3389/fmicb.2015.01409
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Sun, C. L. et al. (2015) Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J . 10.1038/ismej.2015.162
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Tschitschko, B. et al. (2015) Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J 9(9), 2094-107. 10.1038/ismej.2015.110
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Weinmaier, T. et al. (2015) A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome 3, 62. 10.1186/s40168-015-0129-y
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Zhou, J. et al. (2015) High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio 6(1). 10.1128/mBio.02288-14
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2014

Aylward, F. O. et al. (2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio 5(6). 10.1128/mBio.02077-14
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Becker, E. A. et al. (2014) Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genet 10(11), e1004784. 10.1371/journal.pgen.1004784
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Coleman-Derr, D. et al. (2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5(283), 283. 10.3389/fmicb.2014.00283
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Hawley, E. R. et al. (2014) Metagenomic sequencing of two salton sea microbiomes. Genome Announc 2(1). 10.1128/genomeA.01208-13
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Hawley, E. R. et al. (2014) Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar Genomics . 10.1016/j.margen.2014.06.003
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Hawley, E. R. et al. (2014) Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci 9(3), 1259-74. 10.4056/sigs.5029016
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Howe, A. C. et al. (2014) Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 111(13), 4904-9. 10.1073/pnas.1402564111
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Jansson, J. K. et al. (2014) The microbial ecology of permafrost. Nat Rev Microbiol 12(6), 414-25. 10.1038/nrmicro3262
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Jay, Z. J. et al. (2014) Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 80(1), 294-305. 10.1128/AEM.02860-13
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Lamendella, R. et al. (2014) Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 5, 130. 10.3389/fmicb.2014.00130
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Lim, Y. W. et al. (2014) Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J Vis Exp (94). 10.3791/52117
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O'Connor, R. M. et al. (2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A 111(47), E5096-104. 10.1073/pnas.1413110111
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Prestat, E. et al. (2014) FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res . 10.1093/nar/gku702
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Reddy, T. B. et al. (2014) The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res . 10.1093/nar/gku950
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Scholz, M. et al. (2014) Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Sci Rep 4, 6480. 10.1038/srep06480
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Shilova, I. N. et al. (2014) A microarray for assessing transcription from pelagic marine microbial taxa. ISME J . 10.1038/ismej.2014.1
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Simmons, C. W. et al. (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7(1), 495. 10.1186/s13068-014-0180-0
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Singh, G. et al. (2014) Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia. J Clin Microbiol 52(7), 2430-8. 10.1128/JCM.01626-13
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Tas, N. et al. (2014) Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. ISME J . 10.1038/ismej.2014.36
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Wagner, M. R. et al. (2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17(6), 717-26. 10.1111/ele.12276
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Williams, T. J. et al. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J . 10.1038/ismej.2014.18
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Wilson, M. C. et al. (2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506(7486), 58-62. 10.1038/nature12959
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Wu, Y. W. et al. (2014) MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2, 26. 10.1186/2049-2618-2-26
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Xie, G. et al. (2014) Recruiting human microbiome shotgun data to site-specific reference genomes. PLoS One 9(1), e84963. 10.1371/journal.pone.0084963
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2013

Allers, E. et al. (2013) Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean. ISME J 7(2), 256-68. 10.1038/ismej.2012.108
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Aylward, F. O. et al. (2013) Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol 79(12), 3770-8. 10.1128/AEM.03833-12
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D'Haeseleer, P. et al. (2013) Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 8(7), e68465. 10.1371/journal.pone.0068465
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Dodsworth, J. A. et al. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4, 1854. 10.1038/ncomms2884
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He, S. et al. (2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One 8(4), e61126. 10.1371/journal.pone.0061126
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Hug, L.A et al. (2013) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1(1), 22. 10.1186/2049-2618-1-22.
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Inskeep, W. P. et al. (2013) Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Front Microbiol 4, 95. 10.3389/fmicb.2013.00095
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Inskeep, W. P. et al. (2013) The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Front Microbiol 4, 67. 10.3389/fmicb.2013.00067
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Klatt, C. G. et al. (2013) Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol 4, 106. 10.3389/fmicb.2013.00106
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Kozubal, M. A. et al. (2013) Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J 7(3), 622-34. 10.1038/ismej.2012.132
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Lindemann, S. R. et al. (2013) The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol 4, 323. 10.3389/fmicb.2013.00323
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Nurk, S. et al. (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20(10), 714-37. 10.1089/cmb.2013.0084
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Peacock, J. P. et al. (2013) Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS One 8(3), e59927. 10.1371/journal.pone.0059927
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Peiffer, J. A. et al. (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci U S A 110(16), 6548-53. 10.1073/pnas.1302837110
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Rivers, A. R. et al. (2013) Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J . 10.1038/ismej.2013.129
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Romano, C. et al. (2013) Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. Appl Environ Microbiol 79(9), 2932-43. 10.1128/AEM.03591-12
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Scully, E. D. et al. (2013) Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS One 8(9), e73827. 10.1371/journal.pone.0073827
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Shi, W. B. et al. (2013) Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications. PLoS Genet 9(1). Artn E1003131Doi 10.1371/Journal.Pgen.1003131
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2012

Aylward, F. O. et al. (2012) Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J 6(9), 1688-701. 10.1038/ismej.2012.10
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Baelum, J. et al. (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9), 2405-16. 10.1111/j.1462-2920.2012.02780.x
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Berg Miller, M. E. et al. (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14(1), 207-27. 10.1111/j.1462-2920.2011.02593.x
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Brisson, V. L. et al. (2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6(9), 1702-14. 10.1038/ismej.2012.15
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Burow, L. C. et al. (2012) Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J 6(4), 863-74. 10.1038/ismej.2011.142
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DeAngelis, K. M. et al. (2012) Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. MBio 3(1). 10.1128/mBio.00249-11
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Dunbar, J. et al. (2012) Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide. Environ Microbiol 14(5), 1145-58. 10.1111/j.1462-2920.2011.02695.x
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Garcia-Amado, M. A. et al. (2012) Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris). Microb Ecol 63(4), 719-25. 10.1007/s00248-011-9963-z
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Gladden, J. M. et al. (2012) Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass-adapted bacterial consortia. Biotechnol Bioeng 109(5), 1140-5. 10.1002/bit.24388
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Godoy-Vitorino, F. et al. (2012) Differences in crop bacterial community structure between hoatzins from different geographical locations. Research in Microbiology 163(3), 211-220. DOI 10.1016/j.resmic.2012.01.001
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Godoy-Vitorino, F. et al. (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6(3), 531-41. 10.1038/ismej.2011.131
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Graham, D. E. et al. (2012) Microbes in thawing permafrost: the unknown variable in the climate change equation. ISME J 6(4), 709-12. 10.1038/ismej.2011.163
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Harhangi, H. R. et al. (2012) Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol 78(3), 752-8. 10.1128/AEM.07113-11
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Hollister, E. B. et al. (2012) Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One 7(6), e39689. 10.1371/journal.pone.0039689
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Human Microbiome Project, Consortium et al. (2012) A framework for human microbiome research. Nature 486(7402), 215-21. 10.1038/nature11209
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Human Microbiome Project, Consortium et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207-14. 10.1038/nature11234
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Knight, R. et al. (2012) Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology 30(6), 513-520. Doi 10.1038/Nbt.2235
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Lundberg, D. S. et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488(7409), 86-90. 10.1038/nature11237
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Luo, C. et al. (2012) Individual genome assembly from complex community short-read metagenomic datasets. ISME J 6(4), 898-901. 10.1038/ismej.2011.147
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Luo, C. et al. (2012) Individual genome assembly from complex community short-read metagenomic datasets. ISME J 6(4), 898-901. 10.1038/ismej.2011.147
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Markowitz, V. M. et al. (2012) IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 40(Database issue), D123-9. 10.1093/nar/gkr975
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Markowitz, V. M. et al. (2012) IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One 7(7), e40151. 10.1371/journal.pone.0040151
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Orsi, W. et al. (2012) Effect of oxygen minimum zone formation on communities of marine protists. ISME J 6(8), 1586-601. 10.1038/ismej.2012.7
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Pell, J. et al. (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A 109(33), 13272-7. 10.1073/pnas.1121464109
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Scholz, M. B. et al. (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23(1), 9-15. 10.1016/j.copbio.2011.11.013
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Sessitsch, A. et al. (2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions 25(1), 28-36. Doi 10.1094/Mpmi-08-11-0204
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Sessitsch, A. et al. (2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions 25(1), 28-36. Doi 10.1094/Mpmi-08-11-0204
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Steven, B. et al. (2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ Microbiol Rep 4(2), 248-56. 10.1111/j.1758-2229.2012.00328.x
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Swingley, W. D. et al. (2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem. Plos One 7(6). ARTN e38108 DOI 10.1371/journal.pone.0038108
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van der Lelie, D. et al. (2012) The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 7(5), e36740. 10.1371/journal.pone.0036740
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Woebken, D. et al. (2012) Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. Isme Journal 6(7), 1427-1439. DOI 10.1038/ismej.2011.200
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Worden, A. Z. et al. (2012) Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol 22(17), R675-7. 10.1016/j.cub.2012.07.054
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2011

Adams, A. S. et al. (2011) Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J 5(8), 1323-31. 10.1038/ismej.2011.14
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Burnum, K. E. et al. (2011) Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. Isme Journal 5(1), 161-164. DOI 10.1038/ismej.2010.97
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Chain, P. S. et al. (2011) Genomics for key players in the N cycle from guinea pigs to the next frontier. Methods Enzymol 496, 289-318. 10.1016/B978-0-12-386489-5.00012-9
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DeAngelis, K. M. et al. (2011) Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil. Plos One 6(4). ARTN e19306 DOI 10.1371/journal.pone.0019306
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Duhaime, M. B. et al. (2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Stand Genomic Sci 4(2), 271-85. 10.4056/sigs.621069
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Gladden, J. M. et al. (2011) Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass. Applied and Environmental Microbiology 77(16), 5804-5812. Doi 10.1128/Aem.00032-11
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Hess, M. et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331(6016), 463-7. 10.1126/science.1200387
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Huang, Y. J. et al. (2011) Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 127(2), 372-381 e1-3. 10.1016/j.jaci.2010.10.048
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Lykidis, A. et al. (2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J 5(1), 122-30. 10.1038/ismej.2010.125
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Mackelprang, R. et al. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480(7377), 368-71. 10.1038/nature10576
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Pati, A. et al. (2011) ClaMS: A Classifier for Metagenomic Sequences. Stand Genomic Sci 5(2), 248-53. 10.4056/sigs.2075298
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Pope, P. B. et al. (2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333(6042), 646-8. 10.1126/science.1205760
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Reddy, A. P. et al. (2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnol Bioeng 108(9), 2088-98. 10.1002/bit.23176
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Skennerton, C. T. et al. (2011) Phage encoded H-NS: a potential achilles heel in the bacterial defence system. PLoS One 6(5), e20095. 10.1371/journal.pone.0020095
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Swan, B. K. et al. (2011) Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean. Science 333(6047), 1296-1300. DOI 10.1126/science.1203690
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Yilmaz, P. et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology 29(5), 415-420. Doi 10.1038/Nbt.1823
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2010

Allgaier, M. et al. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One 5(1), e8812. 10.1371/journal.pone.0008812
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DeAngelis, K. M. et al. (2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. Bioenergy Research 3(2), 146-158. DOI 10.1007/s12155-010-9089-z
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Hirschman, L. et al. (2010) Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci 2(3), 357-60. 10.4056/sigs.802738
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Kielak, A. et al. (2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol Ecol 71(1), 23-33. 10.1111/j.1574-6941.2009.00785.x
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Kunin, V. et al. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12(1), 118-23. 10.1111/j.1462-2920.2009.02051.x
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Ochman, H. et al. (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol 8(11), e1000546. 10.1371/journal.pbio.1000546
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Pope, P. B. et al. (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 107(33), 14793-8. 10.1073/pnas.1005297107
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2008

Blow, M. J. et al. (2008) Identification of ancient remains through genomic sequencing. Genome Research 18(8), 1347-1353. DOI 10.1101/gr.076091.108
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Dalevi, D. et al. (2008) Annotation of metagenome short reads using proxygenes. Bioinformatics 24(16), I7-I13. DOI 10.1093/bioinformatics/btn276
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Garrity, G. M. et al. (2008) Toward a standards-compliant genomic and metagenomic publication record. OMICS 12(2), 157-60. 10.1089/omi.2008.A2B2
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Hugenholtz, P. et al. (2008) Microbiology - Metagenomics. Nature 455(7212), 481-483. Doi 10.1038/455481a
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Kunin, V. et al. (2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research 18(2), 293-297. Doi 10.1101/Gr.6835308
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Kunin, V. et al. (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4, 198. 10.1038/msb.2008.35
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Markowitz, V. M. et al. (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Research 36, D534-D538. Doi 10.1093/Nar/Gkm869
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Schoenfeld, T. et al. (2008) Assembly of viral metagenomes from yellowstone hot springs. Appl Environ Microbiol 74(13), 4164-74. 10.1128/AEM.02598-07
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Tringe, S. G. et al. (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11(5), 442-6. 10.1016/j.mib.2008.09.011
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Tringe, S. G. et al. (2008) The airborne metagenome in an indoor urban environment. PLoS One 3(4), e1862. 10.1371/journal.pone.0001862
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Wrighton, K. C. et al. (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. Isme Journal 2(11), 1146-1156. DOI 10.1038/ismej.2008.48
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2006

Markowitz, V. M. et al. (2006) An experimental metagenome data management and analysis system. Bioinformatics 22(14), e359-67. 10.1093/bioinformatics/btl217
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Bell, Emma et al. Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. The ISME Journal , 1-11. 10.1038/s41396-022-01207-w
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Diamond, Spencer et al. Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). The ISME Journal , 1-15. 10.1038/s41396-021-01177-5
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Villada, Juan C. et al. The endosymbiotic box of protective tricks. Nature Reviews Microbiology 20(5), 255-255. 10.1038/s41579-022-00727-8
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Wang, Ying et al. Small partners, big impacts. Nature Reviews Microbiology 20(3), 127-127. 10.1038/s41579-022-00693-1
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