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A catalog of reference genomes from the human microbiome.

ABSTRACT: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

SUBMITTER: Human Microbiome Jumpstart Reference Strains Consortium

PROVIDER: S-EPMC2940224 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

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A catalog of reference genomes from the human microbiome.

Nelson Karen E KE Weinstock George M GM Highlander Sarah K SK Worley Kim C KC Creasy Heather Huot HH Wortman Jennifer Russo JR Rusch Douglas B DB Mitreva Makedonka M Sodergren Erica E Chinwalla Asif T AT Feldgarden Michael M Gevers Dirk D Haas Brian J BJ Madupu Ramana R Ward Doyle V DV Birren Bruce W BW Gibbs Richard A RA Methe Barbara B Petrosino Joseph F JF Strausberg Robert L RL Sutton Granger G GG White Owen R OR Wilson Richard K RK Durkin Scott S Giglio Michelle Gwinn MG Gujja Sharvari S Howarth Clint C Kodira Chinnappa D CD Kyrpides Nikos N Mehta Teena T Muzny Donna M DM Pearson Matthew M Pepin Kymberlie K Pati Amrita A Qin Xiang X Yandava Chandri C Zeng Qiandong Q Zhang Lan L Berlin Aaron M AM Chen Lei L Hepburn Theresa A TA Johnson Justin J McCorrison Jamison J Miller Jason J Minx Pat P Nusbaum Chad C Russ Carsten C Sykes Sean M SM Tomlinson Chad M CM Young Sarah S Warren Wesley C WC Badger Jonathan J Crabtree Jonathan J Markowitz Victor M VM Orvis Joshua J Cree Andrew A Ferriera Steve S Fulton Lucinda L LL Fulton Robert S RS Gillis Marcus M Hemphill Lisa D LD Joshi Vandita V Kovar Christie C Torralba Manolito M Wetterstrand Kris A KA Abouellleil Amr A Wollam Aye M AM Buhay Christian J CJ Ding Yan Y Dugan Shannon S FitzGerald Michael G MG Holder Mike M Hostetler Jessica J Clifton Sandra W SW Allen-Vercoe Emma E Earl Ashlee M AM Farmer Candace N CN Liolios Konstantinos K Surette Michael G MG Xu Qiang Q Pohl Craig C Wilczek-Boney Katarzyna K Zhu Dianhui D

Science (New York, N.Y.) 20100501 5981

The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present resul ...[more]

PMID: 20489017

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Project description:BackgroundMetagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.MethodsWe assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM).ResultsHRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition.ConclusionsBy including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available ( www.mbiomenet.org/HRGM/ ). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota.

Dataset Information

A catalog of reference genomes from the human microbiome.

Publications

A catalog of reference genomes from the human microbiome.

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