A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D.

doi:10.1038/s41587-020-0603-3

Title: A unified catalog of 204,938 reference genomes from the human gut microbiome

Journal Article · 19 July 2020 · Nature Biotechnology

DOI: https://doi.org/10.1038/s41587-020-0603-3 · OSTI ID:1756348

^[1]; Nayfach, Stephen ^[2]; Boland, Miguel ^[3];

^[4];

^[3]; Shi, Zhou Jason ^[5];

^[6]; Sakharova, Ekaterina ^[3];

^[7];

^[8];

^[2];

^[3]

European Molecular Biology Lab. (EMBL), Hinxton (United Kingdom). European Bioinformatics Institute; Wellcome Sanger Inst., Hinxton (United Kingdom)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
European Molecular Biology Lab. (EMBL), Hinxton (United Kingdom). European Bioinformatics Institute
Enterome Bioscience, Paris (France)
Gladstone Institutes, San Francisco, CA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States)
Gladstone Institutes, San Francisco, CA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States); Univ. of California, San Francisco, CA (United States)
Univ. of Queensland, Brisbane, QLD (Australia)
Univ. of Trento (Italy)

Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Biotechnology and Biological Sciences Research Council; European Research Council (ERC); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1756348

Journal Information:: Nature Biotechnology, Journal Name: Nature Biotechnology Journal Issue: 1 Vol. 39; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (76)

Effsize - a package for efficient effect size computation Torchiano, Marco https://doi.org/10.5281/zenodo.1480624	software	November 2016
Single-cell metagenomics: challenges and applications Xu, Yuan; Zhao, Fangqing Protein & Cell, Vol. 9, Issue 5 https://doi.org/10.1007/s13238-018-0544-5	journal	April 2018
It's all relative: analyzing microbiome data as compositions Gloor, Gregory B.; Wu, Jia Rong; Pawlowsky-Glahn, Vera Annals of Epidemiology, Vol. 26, Issue 5 https://doi.org/10.1016/j.annepidem.2016.03.003	journal	May 2016
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena Cell, Vol. 176, Issue 3 https://doi.org/10.1016/j.cell.2019.01.001	journal	January 2019
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon The ISME Journal, Vol. 11, Issue 12 https://doi.org/10.1038/ismej.2017.126	journal	July 2017
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
Structure, function and diversity of the healthy human microbiome Nature, Vol. 486, Issue 7402, p. 207-214 https://doi.org/10.1038/nature11234	journal	June 2012
A metagenome-wide association study of gut microbiota in type 2 diabetes Qin, Junjie; Li, Yingrui; Cai, Zhiming Nature, Vol. 490, Issue 7418 https://doi.org/10.1038/nature11450	journal	September 2012
Genomic variation landscape of the human gut microbiome Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi Nature, Vol. 493, Issue 7430 https://doi.org/10.1038/nature11711	journal	December 2012
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Browne, Hilary P.; Forster, Samuel C.; Anonye, Blessing O. Nature, Vol. 533, Issue 7604 https://doi.org/10.1038/nature17645	journal	May 2016
An integrated catalog of reference genes in the human gut microbiome Li, Junhua; Jia, Huijue; Cai, Xianghang Nature Biotechnology, Vol. 32, Issue 8 https://doi.org/10.1038/nbt.2942	journal	July 2014
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks, Donovan H.; Chuvochina, Maria; Waite, David W. Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4229	journal	August 2018
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
Gut microbiome development along the colorectal adenoma–carcinoma sequence Feng, Qiang; Liang, Suisha; Jia, Huijue Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7528	journal	March 2015
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug Wu, Hao; Esteve, Eduardo; Tremaroli, Valentina Nature Medicine, Vol. 23, Issue 7 https://doi.org/10.1038/nm.4345	journal	May 2017
Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention Liu, Ruixin; Hong, Jie; Xu, Xiaoqiang Nature Medicine, Vol. 23, Issue 7 https://doi.org/10.1038/nm.4358	journal	June 2017
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Culture of previously uncultured members of the human gut microbiota by culturomics Lagier, Jean-Christophe; Khelaifia, Saber; Alou, Maryam Tidjani Nature Microbiology, Vol. 1, Issue 12 https://doi.org/10.1038/nmicrobiol.2016.203	journal	November 2016
Clustering huge protein sequence sets in linear time Steinegger, Martin; Söding, Johannes Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04964-5	journal	June 2018
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07641-9	journal	November 2018
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy Sieber, Christian M. K.; Probst, Alexander J.; Sharrar, Allison Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0171-1	journal	May 2018
A new genomic blueprint of the human gut microbiota Almeida, Alexandre; Mitchell, Alex L.; Boland, Miguel Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-0965-1	journal	February 2019
New insights from uncultivated genomes of the global human gut microbiome Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-1058-x	journal	March 2019
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses Zou, Yuanqiang; Xue, Wenbin; Luo, Guangwen Nature Biotechnology, Vol. 37, Issue 2 https://doi.org/10.1038/s41587-018-0008-8	journal	February 2019
A human gut bacterial genome and culture collection for improved metagenomic analyses Forster, Samuel C.; Kumar, Nitin; Anonye, Blessing O. Nature Biotechnology, Vol. 37, Issue 2 https://doi.org/10.1038/s41587-018-0009-7	journal	February 2019
Ultrafast search of all deposited bacterial and viral genomic data Bradley, Phelim; den Bakker, Henk C.; Rocha, Eduardo P. C. Nature Biotechnology, Vol. 37, Issue 2 https://doi.org/10.1038/s41587-018-0010-1	journal	February 2019
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0202-3	journal	August 2019
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research Poyet, M.; Groussin, M.; Gibbons, S. M. Nature Medicine, Vol. 25, Issue 9 https://doi.org/10.1038/s41591-019-0559-3	journal	September 2019
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
Fast and accurate long-read alignment with Burrows–Wheeler transform Li, Heng; Durbin, Richard Bioinformatics, Vol. 26, Issue 5 https://doi.org/10.1093/bioinformatics/btp698	journal	January 2010
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome Nayfach, Stephen; Fischbach, Michael A.; Pollard, Katherine S. Bioinformatics, Vol. 31, Issue 20 https://doi.org/10.1093/bioinformatics/btv382	journal	June 2015
Roary: rapid large-scale prokaryote pan genome analysis Page, Andrew J.; Cummins, Carla A.; Hunt, Martin Bioinformatics, Vol. 31, Issue 22 https://doi.org/10.1093/bioinformatics/btv421	journal	July 2015
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
Integrating long-range connectivity information into de Bruijn graphs Turner, Isaac; Garimella, Kiran V.; Iqbal, Zamin Bioinformatics, Vol. 34, Issue 15 https://doi.org/10.1093/bioinformatics/bty157	journal	March 2018
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt Molecular Biology and Evolution, Vol. 32, Issue 1 https://doi.org/10.1093/molbev/msu300	journal	November 2014
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro Molecular Biology and Evolution, Vol. 34, Issue 8 https://doi.org/10.1093/molbev/msx148	journal	April 2017
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
Expanded microbial genome coverage and improved protein family annotation in the COG database Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1223	journal	November 2014
Assembly: a resource for assembled genomes at NCBI Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1226	journal	November 2015
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center Wattam, Alice R.; Davis, James J.; Assaf, Rida Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1017	journal	November 2016
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families Kalvari, Ioanna; Argasinska, Joanna; Quinones-Olvera, Natalia Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1038	journal	November 2017
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 2018
Interactive Tree Of Life (iTOL) v4: recent updates and new developments Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz239	journal	April 2019
Reclassification of Eubacterium rectale (Hauduroy et al. 1937) Prévot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows Rosero, Jaime A.; Killer, Jirˇí; Sechovcová, Hana International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 2 https://doi.org/10.1099/ijsem.0.000788	journal	February 2016
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Accurate and complete genomes from metagenomes Chen, Lin-Xing; Anantharaman, Karthik; Shaiber, Alon Genome Research, Vol. 30, Issue 3 https://doi.org/10.1101/gr.258640.119	journal	March 2020
A Catalog of Reference Genomes from the Human Microbiome Nelson, K. E.; Weinstock, G. M.; Highlander, S. K. Science, Vol. 328, Issue 5981 https://doi.org/10.1126/science.1183605	journal	May 2010
A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome Armour, Courtney R.; Nayfach, Stephen; Pollard, Katherine S. mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/mSystems.00332-18	journal	May 2019
Antibiotics-induced monodominance of a novel gut bacterial order Hildebrand, Falk; Moitinho-Silva, Lucas; Blasche, Sonja Gut, Vol. 68, Issue 10 https://doi.org/10.1136/gutjnl-2018-317715	journal	January 2019
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Versatile and open software for comparing large genomes Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L. Genome Biology, Vol. 5, Issue 2, R12 https://doi.org/10.1186/gb-2004-5-2-r12	journal	January 2004
Multiple levels of the unknown in microbiome research Thomas, Andrew Maltez; Segata, Nicola BMC Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12915-019-0667-z	journal	June 2019
Mash: fast genome and metagenome distance estimation using MinHash Ondov, Brian D.; Treangen, Todd J.; Melsted, Páll Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0997-x	journal	June 2016
Improved metagenomic analysis with Kraken 2 Wood, Derrick E.; Lu, Jennifer; Langmead, Ben Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1891-0	journal	November 2019
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing Noyes, Noelle R.; Weinroth, Maggie E.; Parker, Jennifer K. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0361-8	journal	October 2017
fastcluster : Fast Hierarchical, Agglomerative Clustering Routines for R and Python Müllner, Daniel Journal of Statistical Software, Vol. 53, Issue 9 https://doi.org/10.18637/jss.v053.i09	journal	January 2013
Effsize - a package for efficient effect size computation Torchiano, Marco https://doi.org/10.5281/ZENODO.1480624	software	November 2016
Mash: fast genome and metagenome distance estimation using MinHash Ondov, Brian; Treangen, Todd; Melsted, Pรกll Figshare https://doi.org/10.6084/m9.figshare.c.3635585	collection	January 2016
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing Noyes, Noelle; Weinroth, Maggie; Parker, Jennifer Figshare https://doi.org/10.6084/m9.figshare.c.3907102	collection	January 2017
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria Di Rienzi, Sara C.; Sharon, Itai; Wrighton, Kelly C. eLife, Vol. 2 https://doi.org/10.7554/eLife.01102	journal	October 2013
Bracken: estimating species abundance in metagenomics data Lu, Jennifer; Breitwieser, Florian P.; Thielen, Peter PeerJ Computer Science, Vol. 3 https://doi.org/10.7717/peerj-cs.104	journal	January 2017
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7359	journal	January 2019

Cited By (14)

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog Borderes, Marianne; Gasc, Cyrielle; Prestat, Emmanuel NAR Genomics and Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1093/nargab/lqab009	journal	January 2021
Additional file 1 of A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome Zhang, Dengwei; Zhang, Jian; Kalimuthu, Shanthini figshare https://doi.org/10.6084/m9.figshare.22705967.v1	dataset	January 2023
Additional file 2 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930275	dataset	January 2023
Additional file 3 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930278	dataset	January 2023
Additional file 4 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930281.v1	dataset	January 2023
Additional file 5 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930284.v1	dataset	January 2023
Additional file 6 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930287.v1	dataset	January 2023
Additional file 7 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930290.v1	dataset	January 2023
Additional file 8 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930293	dataset	January 2023
Additional file 9 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930296.v1	dataset	January 2023
Additional file 10 of Maast: genotyping thousands of microbial strains efficiently Shi, Zhou Jason; Nayfach, Stephen; Pollard, Katherine S. figshare https://doi.org/10.6084/m9.figshare.23930299	dataset	January 2023
Additional file 1 of Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi Cunningham-Oakes, Edward; Bronowski, Christina; Chinyama, End figshare https://doi.org/10.6084/m9.figshare.24587599	dataset	January 2023
Additional file 1 of Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes Ren, Yi; Chen, Lei; Guo, Ruochun figshare https://doi.org/10.6084/m9.figshare.25286900	dataset	January 2024
Additional file 1 of Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies Feng, Xiaowen; Li, Heng figshare https://doi.org/10.6084/m9.figshare.25591343	dataset	January 2024

Similar Records

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

Journal Article · 2023 · Microbiome · OSTI ID:2422515

Leleiwi, Ikaia; Rodriguez-Ramos, Josué; Shaffer, Michael; +9 more

New insights from uncultivated genomes of the global human gut microbiome

Journal Article · 2019 · Nature (London) · OSTI ID:1572809

Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha; +2 more

A continuous fluorescence assay for simple quantification of bile salt hydrolase activity in the gut microbiome

Journal Article · 2019 · Scientific Reports · OSTI ID:1501853

Brandvold, Kristoffer R.; Weaver, Jacqueline M.; Whidbey, Christopher; +1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: A unified catalog of 204,938 reference genomes from the human gut microbiome

Citation Formats

References (76)

Cited By (14)

Similar Records

Related Subjects