A human gut microbial gene catalogue established by metagenomic sequencing
- PMID: 20203603
- PMCID: PMC3779803
- DOI: 10.1038/nature08821
A human gut microbial gene catalogue established by metagenomic sequencing
Abstract
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
Figures
![Figure 1](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0001.gif)
![Figure 2](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0002.gif)
![Figure 3](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0003.gif)
![Figure 4](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0004.gif)
![Figure 5](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0005.gif)
![Figure 6](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/3779803/bin/emss-54210-f0006.gif)
Comment in
-
A gut feeling for disease.Nat Rev Genet. 2010 Apr;11(4):237. doi: 10.1038/nrg2767. Nat Rev Genet. 2010. PMID: 21488225 No abstract available.
Similar articles
-
Mining biomass-degrading genes through Illumina-based de novo sequencing and metagenomic analysis of free-living bacteria in the gut of the lower termite Coptotermes gestroi harvested in Vietnam.J Biosci Bioeng. 2014 Dec;118(6):665-71. doi: 10.1016/j.jbiosc.2014.05.010. Epub 2014 Jun 11. J Biosci Bioeng. 2014. PMID: 24928651
-
Binning metagenomic contigs by coverage and composition.Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14. Nat Methods. 2014. PMID: 25218180
-
[Metagenomics of the intestinal microbiota: potential applications].Gastroenterol Clin Biol. 2010 Sep;34 Suppl 1:S23-8. doi: 10.1016/S0399-8320(10)70017-8. Gastroenterol Clin Biol. 2010. PMID: 20889001 French.
-
Gastrointestinal microbiology enters the metagenomics era.Curr Opin Gastroenterol. 2008 Jan;24(1):4-10. doi: 10.1097/MOG.0b013e3282f2b0e8. Curr Opin Gastroenterol. 2008. PMID: 18043225 Review.
-
Diversity and genomes of uncultured microbial symbionts in the termite gut.Biosci Biotechnol Biochem. 2010;74(6):1145-51. doi: 10.1271/bbb.100094. Epub 2010 Jun 7. Biosci Biotechnol Biochem. 2010. PMID: 20530908 Review.
Cited by
-
Quantifying fecal and plasma short-chain fatty acids in healthy Thai individuals.Comput Struct Biotechnol J. 2024 May 8;23:2163-2172. doi: 10.1016/j.csbj.2024.05.007. eCollection 2024 Dec. Comput Struct Biotechnol J. 2024. PMID: 38827233 Free PMC article.
-
The microbiota-gut-brain-immune interface in the pathogenesis of neuroinflammatory diseases: a narrative review of the emerging literature.Front Immunol. 2024 May 16;15:1365673. doi: 10.3389/fimmu.2024.1365673. eCollection 2024. Front Immunol. 2024. PMID: 38817603 Free PMC article. Review.
-
Novel therapeutic strategy for obesity through the gut microbiota-brain axis: A review article.Caspian J Intern Med. 2024 Spring;15(2):215-227. doi: 10.22088/cjim.15.2.215. Caspian J Intern Med. 2024. PMID: 38807723 Free PMC article. Review.
-
The Gut and the Translocated Microbiomes in HIV Infection: Current Concepts and Future Avenues.Pathog Immun. 2024 May 24;9(1):168-194. doi: 10.20411/pai.v9i1.693. eCollection 2024. Pathog Immun. 2024. PMID: 38807656 Free PMC article. Review.
-
Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction.Nat Commun. 2024 May 28;15(1):4155. doi: 10.1038/s41467-024-48355-5. Nat Commun. 2024. PMID: 38806467 Free PMC article. Clinical Trial.
References
-
- Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–848. doi:S0092-8674(06)00192-9 [pii]10.1016/j.cell.2006.02.017. - PubMed
-
- Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920. doi:307/5717/1915 [pii]10.1126/science.1104816. - PubMed
-
- Hooper LV, Midtvedt T, Gordon JI. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr. 2002;22:283–307. doi:10.1146/annurev.nutr.22.011602.092259011602.092259 [pii] - PubMed
-
- Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–1023. doi:4441022a [pii]10.1038/4441022a. - PubMed
-
- Turnbaugh PJ, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. doi:nature05414 [pii]10.1038/nature05414. - PubMed
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources