2019
(2019) Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.
Nat Microbiol 4(4), 603-613.
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(2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi.
ISME J .
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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) 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) 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) 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) 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) 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) 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.
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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 .
10.1038/s41586-019-1058-x
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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) 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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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.
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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.
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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.
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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.
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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.
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(2018) Metagenomic insights into diazotrophic communities across Arctic glacier forefields.
FEMS Microbiol Ecol .
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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.
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(2018) A viral reckoning: viruses emerge as essential manipulators of global ecosystems.
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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.
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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).
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(2018) Landscape topography structures the soil microbiome in arctic polygonal tundra.
Nat Commun 9(1), 777.
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(2018) Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.
Msystems 3(5), 21.
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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.
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(2018) A most wanted list of conserved microbial protein families with no known domains.
Plos One 13(10).
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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.
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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).
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(2017) IMG/M: integrated genome and metagenome comparative data analysis system.
Nucleic Acids Res 45(D1), D507-D516.
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(2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota.
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(2017) Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.
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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.
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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.
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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.
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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).
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(2017) A genomic perspective on stoichiometric regulation of soil carbon cycling.
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(2017) A compendium of multi-omic sequence information from the Saanich Inlet water column.
Sci Data 4, 170160.
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(2017) Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.
Nat Commun 8(1), 1507.
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(2017) Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes.
mSphere 2(5).
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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.
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(2017) Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders.
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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.
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(2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.
PeerJ 5, e3134.
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(2017) Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.
PeerJ 5, e3134.
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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.
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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.
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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).
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(2017) Lignocellulose pretreatment in a fungus-cultivating termite.
Proc Natl Acad Sci U S A 114(18), 4709-4714.
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(2017) Lignocellulose pretreatment in a fungus-cultivating termite.
Proc Natl Acad Sci U S A 114(18), 4709-4714.
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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.
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(2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
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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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(2017) Giant viruses with an expanded complement of translation system components.
Science 356(6333), 82-85.
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(2017) Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Nat Methods 14(11), 1063-1071.
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(2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
Microbiome 5(1), 65.
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(2017) Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
Microbiome 5(1), 65.
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(2017) NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.
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(2017) Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
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(2017) Succession in the petroleum reservoir microbiome through an oil field production lifecycle.
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(2017) Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico.
Sci Rep 7(1), 16015.
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(2017) Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico.
Sci Rep 7(1), 16015.
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(2017) Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.
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(2017) DNA-SIP based genome-centric metagenomics identifies key long-chain fatty acid-degrading populations in anaerobic digesters with different feeding frequencies.
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2016
(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.
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(2016) Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.
Frontiers in Microbiology 7, 25.
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(2016) Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.
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(2016) Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria.
Front Microbiol 7, 606.
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(2016) Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation.
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(2016) Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods.
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(2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.
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(2016) The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.
Frontiers in Microbiology 7, 150.
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(2016) Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments.
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(2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
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(2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.
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(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.
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(2016) The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.
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(2016) Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.
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(2016) Microbiome Data Science: Understanding Our Microbial Planet.
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(2016) BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly.
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(2016) Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Frontiers in Microbiology 7, 238.
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(2016) Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3.
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(2016) Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes.
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(2016) Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.
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(2016) Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility.
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(2016) In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.
Sci Rep 6, 31362.
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2015
(2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes.
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Front Microbiol 6, 1205.
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(2015) Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.
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(2015) Similar Microbial Communities Found on Two Distant Seafloor Basalts.
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(2014) Convergent bacterial microbiotas in the fungal agricultural systems of insects.
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(2013) Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean.
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(2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites.
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