2021
(2021) Genomes OnLine Database (GOLD) v.8: overview and updates.
Nucleic Acids Res 49(D1), D723-D733.
10.1093/nar/gkaa983
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(2021) IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.
Nucleic Acids Res 49(D1), D764-D775.
10.1093/nar/gkaa946
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2020
(2020) Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.
Environmental Microbiome 15(1).
10.1186/s40793-019-0352-4
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(2020) Clades of huge phages from across Earth's ecosystems.
Nature 578(7795), 425-431.
10.1038/s41586-020-2007-4
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(2020) Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms.
ISME J .
10.1038/s41396-020-0601-y
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(2020) The environment drives microbial trait variability in aquatic habitats.
Mol Ecol 29(23), 4605-4617.
10.1111/mec.15656
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(2020) Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.
Microbiol Resour Announc 9(1).
10.1128/MRA.01361-19
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(2020) Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil.
Microbiol Resour Announc 9(44).
10.1128/MRA.00895-20
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(2020) Metagenomes in the Borderline Ecosystems of the Antarctic Cryptoendolithic Communities.
Microbiol Resour Announc 9(10).
10.1128/MRA.01599-19
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(2020) Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation.
Commun Biol 3(1), 320.
10.1038/s42003-020-1047-5
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(2020) Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow.
ISME J 14(7), 1834-1846.
10.1038/s41396-020-0655-x
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(2020) Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems.
Msystems 5(2).
10.1128/mSystems.00098-20
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(2020) Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes.
J Ind Microbiol Biotechnol 47(12), 1031-1044.
10.1007/s10295-020-02326-z
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(2020) Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti.
Front Microbiol 10, 3044.
10.3389/fmicb.2019.03044
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(2020) Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters.
ISME J .
10.1038/s41396-020-00825-6
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(2020) A phylogenetically novel cyanobacterium most closely related to Gloeobacter.
ISME J .
10.1038/s41396-020-0668-5
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(2020) A pipeline for targeted metagenomics of environmental bacteria.
Microbiome 8(1), 21.
10.1186/s40168-020-0790-7
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(2020) Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites.
PeerJ 8, e8614.
10.7717/peerj.8614
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(2020) Phage-specific metabolic reprogramming of virocells.
ISME J 14(4), 881-895.
10.1038/s41396-019-0580-z
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(2020) The International Virus Bioinformatics Meeting 2020.
Viruses 12(12).
10.3390/v12121398
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(2020) Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon.
ISME J .
10.1038/s41396-020-00804-x
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(2020) Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters.
Front Microbiol 11.
10.3389/fmicb.2020.593006
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(2020) Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests.
Glob Chang Biol .
10.1111/gcb.15439
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(2020) A genomic catalog of Earth's microbiomes.
Nat Biotechnol .
10.1038/s41587-020-0718-6
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(2020) CheckV assesses the quality and completeness of metagenome-assembled viral genomes.
Nat Biotechnol .
10.1038/s41587-020-00774-7
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(2020) Biases in genome reconstruction from metagenomic data.
PeerJ 8, e10119.
10.7717/peerj.10119
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(2020) Niche differentiation is spatially and temporally regulated in the rhizosphere.
Isme Journal 14(4), 999-1014.
10.1038/s41396-019-0582-x
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(2020) Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla.
PLoS One 15(4), e0231083.
10.1371/journal.pone.0231083
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(2020) Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase.
Front Microbiol 11, 583361.
10.3389/fmicb.2020.583361
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(2020) Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina).
Microbiol Resour Announc 9(41).
10.1128/MRA.00882-20
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(2020) Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria.
ISME J 14(6), 1547-1560.
10.1038/s41396-020-0624-4
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(2020) Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.
Appl Environ Microbiol 86(10).
10.1128/AEM.00140-20
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(2020) In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay.
Microb Ecol .
10.1007/s00248-020-01621-7
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(2020) Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System.
Front Microbiol 11, 1075.
10.3389/fmicb.2020.01075
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(2020) COVID-19 pandemic reveals the peril of ignoring metadata standards.
Sci Data 7(1), 188.
10.1038/s41597-020-0524-5
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(2020) Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus.
mSystems 5(3).
10.1128/mSystems.00048-20
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(2020) Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.
Genome Biology 21(1).
10.1186/s13059-020-02195-w
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(2020) Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research.
Front Microbiol 11, 572131.
10.3389/fmicb.2020.572131
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(2020) In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs.
Sci Total Environ 715, 136646.
10.1016/j.scitotenv.2020.136646
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(2020) High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.
ISME J 14(7), 1857-1872.
10.1038/s41396-020-0650-2
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(2020) Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions.
FEMS Microbiol Ecol 96(5).
10.1093/femsec/fiaa050
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(2020) Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.
Microbiome 8(1), 22.
10.1186/s40168-019-0780-9
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2019
(2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.
Nat Microbiol 4(4), 603-613.
10.1038/s41564-019-0363-3
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(2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.
ISME J .
10.1038/s41396-018-0343-2
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(2019) Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.
Sci Data 6(1), 140.
10.1038/s41597-019-0141-3
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(2019) Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere.
ISME J 13(6), 1457-1468.
10.1038/s41396-019-0352-9
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(2019) Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols.
Appl Environ Microbiol 85(12).
10.1128/AEM.00189-19
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(2019) Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.
Nat Microbiol 4(2), 352-361.
10.1038/s41564-018-0312-6
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(2019) Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.
Nat Microbiol .
10.1038/s41564-019-0449-y
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(2019) Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae.
Syst Appl Microbiol 42(1), 41-53.
10.1016/j.syapm.2018.08.007
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(2019) Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops.
Nat Commun 10(1), 4135.
10.1038/s41467-019-11974-4
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(2019) Unexpected host dependency of Antarctic Nanohaloarchaeota.
Proc Natl Acad Sci U S A .
10.1073/pnas.1905179116
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(2019) Interactions between plants and soil shaping the root microbiome under abiotic stress.
Biochem J 476(19), 2705-2724.
10.1042/BCJ20180615
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(2019) Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes.
mSphere 4(1).
10.1128/mSphere.00436-18
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(2019) Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Sci Data 6(1), 207.
10.1038/s41597-019-0222-3
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(2019) Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.
Nature Biotechnology 37(6), 632-+.
10.1038/s41587-019-0100-8
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(2019) MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.
Peerj 7.
10.7717/peerj.7359
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(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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(2019) Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology.
Trends Microbiol .
10.1016/j.tim.2019.03.003
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(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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(2019) Advancing Genome-Resolved Metagenomics beyond the Shotgun.
mSystems 4(3).
10.1128/mSystems.00118-19
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(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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(2019) Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary.
Biotechniques .
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(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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(2019) Numerous cultivated and uncultivated viruses encode ribosomal proteins.
Nat Commun 10(1), 752.
10.1038/s41467-019-08672-6
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(2019) Novel insights from uncultivated genomes of the global human gut microbiome.
Nature .
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(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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(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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(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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(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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(2019) Optimizing de novo genome assembly from PCR-amplified metagenomes.
PeerJ 7, e6902.
10.7717/peerj.6902
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(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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(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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(2019) SpaRC: scalable sequence clustering using Apache Spark.
Bioinformatics 35(5), 760-768.
10.1093/bioinformatics/bty733
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(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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(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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(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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(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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(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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(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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(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
(2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.
ISME J .
10.1038/s41396-018-0078-0
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(2018) Discovery of enzymes for toluene synthesis from anoxic microbial communities.
Nat Chem Biol .
10.1038/s41589-018-0017-4
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(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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(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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(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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(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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(2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.
Science .
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(2018) Peatland Acidobacteria with a dissimilatory sulfur metabolism.
ISME J .
10.1038/s41396-018-0077-1
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(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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(2018) Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H2-oxidation activity measured in three soils exposed to H2.
Soil Biology and Biochemistry 125, 239-243.
10.1016/j.soilbio.2018.07.020
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(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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(2018) Genomic features of bacterial adaptation to plants.
Nat Genet 50(1), 138-150.
10.1038/s41588-017-0012-9
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(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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(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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(2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields.
FEMS Microbiol Ecol .
10.1093/femsec/fiy114
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(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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(2018) A viral reckoning: viruses emerge as essential manipulators of global ecosystems.
Environ Microbiol Rep .
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(2018) Minimum Information about an Uncultivated Virus Genome (MIUViG).
Nature Biotechnology 37, 29.
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(2018) Hidden diversity of soil giant viruses.
Nature Communications 9, 9.
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(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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(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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(2018) Diversity of Active Viral Infections within the Sphagnum Microbiome.
Appl Environ Microbiol 84(23).
10.1128/AEM.01124-18
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(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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(2018) Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.
Msystems 3(5), 21.
10.1128/mSystems.00076-18
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(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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(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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(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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(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
(2017) Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.
Front Microbiol 8, 2264.
10.3389/fmicb.2017.02264
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(2017) Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.
mSphere 2(4).
10.1128/mSphereDirect.00257-17
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(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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(2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.
ISME J .
10.1038/s41396-017-0002-z
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(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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(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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(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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(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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(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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(2017) A genomic perspective on stoichiometric regulation of soil carbon cycling.
ISME J .
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(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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(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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(2017) Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes.
mSphere 2(5).
10.1128/mSphere.00277-17
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(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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(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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(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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(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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(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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(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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(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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(2017) The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil.
Appl Environ Microbiol 83(11).
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(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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(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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(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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(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 .
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(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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(2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Nat Biotechnol .
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(2017) The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.
MBio 8(1).
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(2017) Protein structure determination using metagenome sequence data.
Science 355(6322), 294-298.
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(2017) Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.
Nat Protoc 12(8), 1673-1682.
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(2017) Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity.
PeerJ 5, e3817.
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(2017) Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.
Nat Commun 8(1), 858.
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(2017) Towards a balanced view of the bacterial tree of life.
Microbiome 5(1), 140.
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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.
Doi 10.1094/Mpmi-08-11-0204
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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.
Doi 10.1094/Mpmi-08-11-0204
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(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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(2012) Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem.
Plos One 7(6).
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(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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(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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(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
(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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(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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(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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(2011) Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil.
Plos One 6(4).
ARTN e19306
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(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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(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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(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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(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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(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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(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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(2011) ClaMS: A Classifier for Metagenomic Sequences.
Stand Genomic Sci 5(2), 248-53.
10.4056/sigs.2075298
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(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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(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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(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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(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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(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
(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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(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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(2010) Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Stand Genomic Sci 2(3), 357-60.
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(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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(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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(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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(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
(2008) Identification of ancient remains through genomic sequencing.
Genome Research 18(8), 1347-1353.
DOI 10.1101/gr.076091.108
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(2008) Annotation of metagenome short reads using proxygenes.
Bioinformatics 24(16), I7-I13.
DOI 10.1093/bioinformatics/btn276
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(2008) Toward a standards-compliant genomic and metagenomic publication record.
OMICS 12(2), 157-60.
10.1089/omi.2008.A2B2
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(2008) Microbiology - Metagenomics.
Nature 455(7212), 481-483.
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(2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal.
Genome Research 18(2), 293-297.
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(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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(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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(2008) Assembly of viral metagenomes from yellowstone hot springs.
Appl Environ Microbiol 74(13), 4164-74.
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(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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(2008) The airborne metagenome in an indoor urban environment.
PLoS One 3(4), e1862.
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(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
(2006) An experimental metagenome data management and analysis system.
Bioinformatics 22(14), e359-67.
10.1093/bioinformatics/btl217
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