Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Abstract
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
- Authors:
-
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- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); United States Dept. of Agriculture, Gainesville, FL (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States)
- Broad Institute, Cambridge, MA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- European Molecular Biology Lab., Heidelberg (Germany)
- The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
- Michigan State Univ., East Lansing, MI (United States)
- California State Univ., San Bernardino, CA (United States)
- J. Craig Venter Institute, San Diego, CA (United States)
- J. Craig Venter Institute, Rockville, MD (United States)
- Max Planck Institute for Marine Microbiology, Bremen (Germany)
- Univ. of Chicago, Chicago, IL (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Univ. of British Columbia, Vancouver, BC (Canada)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Southern California, Los Angeles, CA (United States)
- Uppsala Univ., Uppsala (Sweden)
- Univ. of Vermont Cancer Center, Burlington, VT (United States)
- Georgia Inst. of Technology, Atlanta, GA (United States)
- Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
- Univ. of Texas-Austin, Austin, TX (United States)
- Univ. of Vienna, Vienna (Austria)
- Univ. of California, Davis, CA (United States)
- Univ. of Nevada, Las Vegas, NV (United States)
- Univ. of Wisconsin, Madison, WI (United States)
- Univ. of Colorado, Boulder, CO (United States)
- Univ. of California San Diego, La Jolla, CA (United States)
- European Molecular Biology Lab., Cambridge (United Kingdom)
- National Institutes of Health, Bethesda, MD (United States)
- The Univ. of Queensland, Queensland (Australia)
- National Cancer Institute, Frederick, MD (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
- St. Petersburg State Univ., St. Petersburg (Russia)
- Knapp Center for Biomedical Discovery, Chicago, IL (United States)
- Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1375044
- Alternate Identifier(s):
- OSTI ID: 1394303; OSTI ID: 1414520; OSTI ID: 1459393
- Report Number(s):
- PNNL-SA-125978
Journal ID: ISSN 1087-0156; 137394
- Grant/Contract Number:
- AC02-06CH11357; AC05-00OR22725; AC05-76RL01830; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Biotechnology
- Additional Journal Information:
- Journal Volume: 35; Journal Issue: 8; Journal ID: ISSN 1087-0156
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
Citation Formats
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. United States: N. p., 2017.
Web. doi:10.1038/nbt.3893.
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, & Woyke, Tanja. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. United States. https://doi.org/10.1038/nbt.3893
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen -Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Kyrpides, Nikos C., Schriml, Lynn, Garrity, George M., Hugenholtz, Philip, Sutton, Granger, Yilmaz, Pelin, Meyer, Folker, Glockner, Frank O., Gilbert, Jack A., Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja. Tue .
"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea". United States. https://doi.org/10.1038/nbt.3893. https://www.osti.gov/servlets/purl/1375044.
@article{osti_1375044,
title = {Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea},
author = {Bowers, Robert M. and Kyrpides, Nikos C. and Stepanauskas, Ramunas and Harmon-Smith, Miranda and Doud, Devin and Reddy, T. B. K. and Schulz, Frederik and Jarett, Jessica and Rivers, Adam R. and Eloe-Fadrosh, Emiley A. and Tringe, Susannah G. and Ivanova, Natalia N. and Copeland, Alex and Clum, Alicia and Becraft, Eric D. and Malmstrom, Rex R. and Birren, Bruce and Podar, Mircea and Bork, Peer and Weinstock, George M. and Garrity, George M. and Dodsworth, Jeremy A. and Yooseph, Shibu and Sutton, Granger and Glockner, Frank O. and Gilbert, Jack A. and Nelson, William C. and Hallam, Steven J. and Jungbluth, Sean P. and Ettema, Thijs J. G. and Tighe, Scott and Konstantinidis, Konstantinos T. and Liu, Wen -Tso and Baker, Brett J. and Rattei, Thomas and Eisen, Jonathan A. and Hedlund, Brian and McMahon, Katherine D. and Fierer, Noah and Knight, Rob and Finn, Rob and Cochrane, Guy and Karsch-Mizrachi, Ilene and Tyson, Gene W. and Rinke, Christian and Kyrpides, Nikos C. and Schriml, Lynn and Garrity, George M. and Hugenholtz, Philip and Sutton, Granger and Yilmaz, Pelin and Meyer, Folker and Glockner, Frank O. and Gilbert, Jack A. and Knight, Rob and Finn, Rob and Cochrane, Guy and Karsch-Mizrachi, Ilene and Lapidus, Alla and Meyer, Folker and Yilmaz, Pelin and Parks, Donovan H. and Eren, A. M. and Schriml, Lynn and Banfield, Jillian F. and Hugenholtz, Philip and Woyke, Tanja},
abstractNote = {We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.},
doi = {10.1038/nbt.3893},
journal = {Nature Biotechnology},
number = 8,
volume = 35,
place = {United States},
year = {Tue Aug 08 00:00:00 EDT 2017},
month = {Tue Aug 08 00:00:00 EDT 2017}
}
Web of Science
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Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
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Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake
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Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species
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Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere
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In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes
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Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov
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Genome sequences of horticultural plants: past, present, and future
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Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
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Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis
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Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities
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Microbial abundance, activity and population genomic profiling with mOTUs2
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Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
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Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
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Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2
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A human gut bacterial genome and culture collection for improved metagenomic analyses
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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
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Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community
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Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
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High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea
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Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland
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Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake
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Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
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Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease
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Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of
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Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity
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Four Draft Single-Cell Genome Sequences of Novel, Nearly Identical Kiritimatiellaeota Strains Isolated from the Continental Deep Subsurface
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Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics
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Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs
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Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
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The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities
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Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
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Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
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CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes
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Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP
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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
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Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
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Assessment of urban microbiome assemblies with the help of targeted in silico gold standards
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Integrated multi-omic analysis of host-microbiota interactions in acute oak decline
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Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity
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Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics
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Parasite microbiome project: Grand challenges
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Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism
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Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
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Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes
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Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
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Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments
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Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
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Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments
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Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
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An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids
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Genome of a Novel Bacterium “Candidatus Jettenia ecosi” Reconstructed From the Metagenome of an Anammox Bioreactor
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A Bioinformatics Guide to Plant Microbiome Analysis
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Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
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Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites
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