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






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
-
Effects of Polyvinyl Chloride Microplastics on the Reproductive System, Intestinal Structure, and Microflora in Male and Female Mice.Vet Sci. 2024 Oct 9;11(10):488. doi: 10.3390/vetsci11100488. Vet Sci. 2024. PMID: 39453080 Free PMC article.
-
Multifactorial diversity sustains microbial community stability.ISME J. 2013 Nov;7(11):2126-36. doi: 10.1038/ismej.2013.108. Epub 2013 Jul 4. ISME J. 2013. PMID: 23823494 Free PMC article.
-
Microbiological survey of the human gastric ecosystem using culturing and pyrosequencing methods.Microb Ecol. 2013 Apr;65(3):763-72. doi: 10.1007/s00248-013-0192-5. Epub 2013 Feb 10. Microb Ecol. 2013. PMID: 23397369
-
Could the Gut Microbiota Serve as a Therapeutic Target in Ischemic Stroke?Evid Based Complement Alternat Med. 2021 Apr 17;2021:1391384. doi: 10.1155/2021/1391384. eCollection 2021. Evid Based Complement Alternat Med. 2021. PMID: 33959182 Free PMC article. Review.
-
Endotoxin neutralization as a biomonitor for inflammatory bowel disease.PLoS One. 2013 Jun 24;8(6):e67736. doi: 10.1371/journal.pone.0067736. Print 2013. PLoS One. 2013. PMID: 23826338 Free PMC article.
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
Medical