A Catalog of Reference Genomes from the Human Microbiome
Open accessAbstract
News from the Inner Tube of Life: A major initiative by the U.S. National Institutes of Health to sequence 900 genomes of microorganisms that live on the surfaces and orifices of the human body has established standardized protocols and methods for such large-scale reference sequencing. By combining previously accumulated data with new data, Nelson et al. (p. 994 ) present an initial analysis of 178 bacterial genomes. The sampling so far barely scratches the surface of the microbial diversity found on humans, but the work provides an important baseline for future analyses.
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SagA orthologs are found in humans through alignment of the SagA NlpC/p60 domain with genomes within the Human Microbiome Project.
“We further confirmed that SagA orthologs are found in humans through alignment of the SagA NlpC/p60 domain with genomes within the Human Microbiome Project (24) (Fig. 2C, Table S5).”
From <i>Enterococcus</i> peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy (2021) · cites this paper as [24]
HMP1 yielded community resources including nucleotide sequences of microorganisms and communities, protocols for reproducible body-wide microbiome sampling and data generation, and computational methods for microbiome analysis and epidemiology.
“This first phase of the HMP (HMP1) thus yielded a wealth of community resources: nucleotide sequences of microorganisms and communities from a large number of isolates, individuals, and populations (http://hmpdacc.org)34–37; protocols to support reproducible body-wide microbiome sampling and data generation38–40; and computational methods for microbiome analysis and epidemiology41–47.”
From The Integrative Human Microbiome Project (2019) · cites this paper as [35]
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- Authors
- The Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K. E., Weinstock, G. M., Highlander, S. K., Worley, K. C., Creasy, H. H., Wortman, J. R., Rusch, D. B., Mitreva, M., Sodergren, E., Chinwalla, A. T., Feldgarden, M., Gevers, D., Haas, B. J., Madupu, R., Ward, D. V., Birren, B. W., Gibbs, R. A., Methe, B., Petrosino, J. F., Strausberg, R. L., Sutton, G. G., White, O. R., Wilson, R. K., Durkin, S., Giglio, M. G., Gujja, S., Howarth, C., Kodira, C. D., Kyrpides, N., Mehta, T., Muzny, D. M., Pearson, M., Pepin, K., Pati, A., Qin, X., Yandava, C., Zeng, Q., Zhang, L., Berlin, A. M., Chen, L., Hepburn, T. A., Johnson, J., McCorrison, J., Miller, J., Minx, P., Nusbaum, C., Russ, C., Sykes, S. M., Tomlinson, C. M., Young, S., Warren, W. C., Badger, J., Crabtree, J., Markowitz, V. M., Orvis, J., Cree, A., Ferriera, S., Fulton, L. L., Fulton, R. S., Gillis, M., Hemphill, L. D., Joshi, V., Kovar, C., Torralba, M., Wetterstrand, K. A., Abouellleil, A., Wollam, A. M., Buhay, C. J., Ding, Y., Dugan, S., FitzGerald, M. G., Holder, M., Hostetler, J., Clifton, S. W., Allen-Vercoe, E., Earl, A. M., Farmer, C. N., Liolios, K., Surette, M. G., Xu, Q., Pohl, C., Wilczek-Boney, K., & Zhu, D.
- ORCID
- Weinstock, George M.
- Highlander, Sarah K.
- Worley, Kim C.
- Wortman, Jennifer Russo
- Rusch, Douglas B.
- Mitreva, Makedonka
- Sodergren, Erica
- Chinwalla, Asif T.
- Feldgarden, Michael
- Gevers, Dirk
- Haas, Brian J.
- Ward, Doyle V.
- Birren, Bruce W.
- Gibbs, Richard A.
- Petrosino, Joseph F.
- Sutton, Granger G.
- White, Owen R.
- Giglio, Michelle Gwinn
- Kyrpides, Nikos
- Muzny, Donna M.
- Pepin, Kymberlie
- Qin, Xiang
- Zeng, Qiandong
- Zhang, Lan
- Chen, Lei
- McCorrison, Jamison
- Miller, Jason
- Nusbaum, Chad
- Tomlinson, Chad M.
- Young, Sarah
- Warren, Wesley C.
- Badger, Jonathan
- Crabtree, Jonathan
- Orvis, Joshua
- Fulton, Lucinda L.
- Fulton, Robert S.
- Torralba, Manolito
- Wetterstrand, Kris A.
- Ding, Yan
- Dugan, Shannon
- FitzGerald, Michael G.
- Earl, Ashlee M.
- Surette, Michael G.
- Pohl, Craig
- Venue
- Science
- Published
- 2010-05-21
- Volume
- 328
- Issue
- 5981
- Pages
- 994-999
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2940224
- OpenAlex
- W2023046869
- Cited by
- 702
- References
- 16
- Citations by year
- 2026: 11 · 2025: 30 · 2024: 29 · 2023: 21 · 2022: 40 · 2021: 45 · 2020: 30 · 2019: 45 · 2018: 31 · 2017: 33 · 2016: 41 · 2015: 51 · 2014: 59 · 2013: 58 · 2012: 70
- FWCI
- 30.47
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Goce Delchev University Repository (Goce Delčev University of Štip) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Funders
- Crohn's and Colitis Foundation
- Broad Institute
- Crohn's and Colitis Foundation of Canada
- Universiteit Gent
- Vlaamse regering
- National Institutes of Health (n01ai30071-19-0-3)
- Canadian Institutes of Health Research
- National Human Genome Research Institute (U54HG003067, U54HG004969, U54HG003079, U54HG003273, U54HG004968, U54HG004973)
- National Institute of Allergy and Infectious Diseases (HHSN272200900017C, U54AI084844, N01 AI030071, N01 AI30071)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human microbiome, pan-genome, metagenomics, gastrointestinal microbiome, microbial diversity, genome sequencing
- MeSH terms
- Bacteria, Bacterial Proteins, Genes, Bacterial, Humans, Mouth, Peptides, Phylogeny, Respiratory System, Skin, Urogenital System, Genetic Variation, Genome, Bacterial, Sequence Analysis, DNA, Computational Biology, Genome, Archaeal, Databases, Genetic, Gastrointestinal Tract, Biodiversity, Metagenome, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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