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Science DOI:10.1126/science.1183605

A catalog of reference genomes from the human microbiome.

Publication TypeJournal Article
Year of Publication2010
AuthorsNelson, KE, Weinstock, GM, Highlander, SK, Worley, KC, Creasy, HHuot, Wortman, JRusso, Rusch, DB, Mitreva, M, Sodergren, E, Chinwalla, AT, Feldgarden, M, Gevers, D, Haas, BJ, Madupu, R, Ward, DV, Birren, BW, Gibbs, RA, Methé, B, Petrosino, JF, Strausberg, RL, Sutton, GG, White, OR, Wilson, RK, Durkin, S, Giglio, MGwinn, Gujja, S, Howarth, C, Kodira, CD, Kyrpides, N, Mehta, T, Muzny, DM, Pearson, M, Pepin, K, Pati, A, Qin, X, Yandava, C, Zeng, Q, Zhang, L, Berlin, AM, Chen, L, Hepburn, TA, Johnson, J, McCorrison, J, Miller, J, Minx, P, Nusbaum, C, Russ, C, Sykes, SM, Tomlinson, CM, Young, S, Warren, WC, Badger, J, Crabtree, J, Markowitz, VM, Orvis, J, Cree, A, Ferriera, S, Fulton, LL, Fulton, RS, Gillis, M, Hemphill, LD, Joshi, V, Kovar, C, Torralba, M, Wetterstrand, KA, Abouellleil, A, Wollam, AM, Buhay, CJ, Ding, Y, Dugan, S, FitzGerald, MG, Holder, M, Hostetler, J, Clifton, SW, Allen-Vercoe, E, Earl, AM, Farmer, CN, Liolios, K, Surette, MG, Xu, Q, Pohl, C, Wilczek-Boney, K, Zhu, D
Corporate AuthorsHuman Microbiome Jumpstart Reference Strains Consortium
JournalScience
Volume328
Issue5981
Pages994-9
Date Published2010 May 21
ISSN1095-9203
KeywordsBacteria, Bacterial Proteins, Biodiversity, Computational Biology, Databases, Genetic, Gastrointestinal Tract, Genes, Bacterial, Genetic Variation, Genome, Archaeal, Genome, Bacterial, Humans, Metagenome, Metagenomics, Mouth, Peptides, Phylogeny, Respiratory System, Sequence Analysis, DNA, Skin, Urogenital System
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.

URLhttp://www.sciencemag.org/cgi/pmidlookup?view=short&pmid=20489017
DOI10.1126/science.1183605
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/20489017?dopt=Abstract

Alternate JournalScience
PubMed ID20489017
PubMed Central IDPMC2940224
Grant ListU54-HG003273 / HG / NHGRI NIH HHS / United States
U54 HG004973 / HG / NHGRI NIH HHS / United States
U54-HG004969 / HG / NHGRI NIH HHS / United States
U54 HG003273-05S1 / HG / NHGRI NIH HHS / United States
U54-HG003079 / HG / NHGRI NIH HHS / United States
U54 HG004973-02 / HG / NHGRI NIH HHS / United States
U54 HG003273-04S1 / HG / NHGRI NIH HHS / United States
U54 AI084844 / AI / NIAID NIH HHS / United States
U54 HG003273-05 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
U54 HG003273-05S2 / HG / NHGRI NIH HHS / United States
U54 HG004973-01 / HG / NHGRI NIH HHS / United States
U54-HG004968 / HG / NHGRI NIH HHS / United States
U54 HG004968 / HG / NHGRI NIH HHS / United States
U54 HG003273-08 / HG / NHGRI NIH HHS / United States
U54 HG003273-04 / HG / NHGRI NIH HHS / United States
/ / Canadian Institutes of Health Research / Canada
HHSN272200900017C / / PHS HHS / United States
U54 HG003273-06S1 / HG / NHGRI NIH HHS / United States
U54-AI084844 / AI / NIAID NIH HHS / United States
U54 HG003079 / HG / NHGRI NIH HHS / United States
U54 HG004969 / HG / NHGRI NIH HHS / United States
N01 AI30071 / AI / NIAID NIH HHS / United States
U54 HG003273-07 / HG / NHGRI NIH HHS / United States
U54-HG004973 / HG / NHGRI NIH HHS / United States
HHSN272200900017C / AI / NIAID NIH HHS / United States
U54 HG003273-06 / HG / NHGRI NIH HHS / United States
N01 AI030071 / AI / NIAID NIH HHS / United States
U54 HG003273-06S2 / HG / NHGRI NIH HHS / United States