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Metagenomic Analysis of the Human Distal Gut Microbiome
Open accessAbstract
The human intestinal microbiota is composed of 10(13) to 10(14) microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed approximately 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-d-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
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“Since early studies of environmental and host-associated microbial communities (Gill et al., 2006; Tyson et al., 2004; Venter et al., 2004), it has been clear that many aspects of intercellular and inter-species signaling, short- and long-term evolution, and regulatory programs are exercised by microbes in their natural settings and extremely difficult to recapitulate in a controlled setting.”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Gill et al., 2006
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Nicholson, J. K., Holmes, E., & Wilson, I. D. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1152 · Cited by 945
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An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Self-citationA human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
Self-citationA core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Self-citationEnterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548
Metadata
- Authors
- Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E.
- Affiliations
- Washington University in St. Louis (US)
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
- Corresponding author
- Gill, Steven R.
- Pop, Mihai
- ORCID
- Venue
- Science
- Published
- 2006-06-02
- Volume
- 312
- Issue
- 5778
- Pages
- 1355-1359
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3027896
- OpenAlex
- W2145336165
- Cited by
- 4,699
- References
- 3
- Citations by year
- 2026: 64 · 2025: 183 · 2024: 212 · 2023: 255 · 2022: 330 · 2021: 303 · 2020: 353 · 2019: 285 · 2018: 250 · 2017: 259 · 2016: 245 · 2015: 256 · 2014: 249 · 2013: 254 · 2012: 247
- FWCI
- 68.03
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (AI51259, R01AI051259)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK 70977, R01DK070977)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human gut microbiome, metagenomics, 16S rRNA gene sequencing, fecal DNA, microbial gene content, glycogen metabolism, amino acid metabolism, xenobiotic metabolism, methanogenesis, methylerythritol phosphate pathway, vitamin biosynthesis, isoprenoid biosynthesis
- MeSH terms
- Adult, Bacteria, Bifidobacterium, Dietary Carbohydrates, Dietary Fiber, DNA, Ribosomal, Feces, Female, Fermentation, Humans, Intestinal Mucosa, Intestines, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Genetic Variation, Xenobiotics, Open Reading Frames, Genome, Bacterial, Genomics
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