Skip to main content
PMC home page
Protein & Cell logoLink to Protein & Cell
. 2010 Aug 28;1(8):718–725. doi: 10.1007/s13238-010-0093-z

Human gut microbiome: the second genome of human body

Baoli Zhu 1,✉, Xin Wang 2, Lanjuan Li 3
PMCID: PMC4875195  PMID: 21203913

Abstract

The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50–100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.

References

  1. Ahmed S., Macfarlane G.T., Fite A., McBain A.J., Gilbert P., Macfarlane S. Mucosa-Associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol. 2007;73:7435–7442. doi: 10.1128/AEM.01143-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Aoi Y., Kinoshita T., Hata T., Ohta H., Obokata H., Tsuneda S. Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl Environ Microbiol. 2009;75:3826–3833. doi: 10.1128/AEM.02542-08. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bäckhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., Gordon J.I. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920. doi: 10.1126/science.1104816. [DOI] [PubMed] [Google Scholar]
  4. Bollmann A., Lewis K., Epstein S.S. Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol. 2007;73:6386–6390. doi: 10.1128/AEM.01309-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Child M.W., Kennedy A., Walker A.W., Bahrami B., Macfarlane S., Macfarlane G.T. Studies on the effect of system retention time on bacterial populations colonizing a three-stage continuous culture model of the human large gut using FISH techniques. FEMS Microbiol Ecol. 2006;55:299–310. doi: 10.1111/j.1574-6941.2005.00016.x. [DOI] [PubMed] [Google Scholar]
  6. Davies J. In a map for human life, count the microbes, too. Science. 2001;291:2316. doi: 10.1126/science.291.5512.2316b. [DOI] [PubMed] [Google Scholar]
  7. Eckburg P.B., Bik E.M., Bernstein C.N., Purdom E., Dethlefsen L., Sargent M., Gill S.R., Nelson K.E., Relman D.A. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638. doi: 10.1126/science.1110591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gaboriau-Routhiau V., Rakotobe S., Lécuyer E., Mulder I., Lan A., Bridonneau C., Rochet V., Pisi A., De Paepe M., Brandi G., Eberl G., Snel J., Kelly D., Cerf-Bensussan N. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 2009;31:677–689. doi: 10.1016/j.immuni.2009.08.020. [DOI] [PubMed] [Google Scholar]
  9. Gibson G.R., Wang X. Enrichment of bifidobacteria from human gut contents by oligofructose using continuous culture. FEMS Microbiol Lett. 1994;118:121–127. doi: 10.1111/j.1574-6968.1994.tb06813.x. [DOI] [PubMed] [Google Scholar]
  10. 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. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–1359. doi: 10.1126/science.1124234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Haller D., Jobin C. Interaction between resident luminal bacteria and the host: can a healthy relationship turn sour? J Pediatr Gastroenterol Nutr. 2004;38:123–136. doi: 10.1097/00005176-200402000-00004. [DOI] [PubMed] [Google Scholar]
  12. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–685. doi: 10.1128/MMBR.68.4.669-685.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5:R245–R249. doi: 10.1016/S1074-5521(98)90108-9. [DOI] [PubMed] [Google Scholar]
  14. Hayashi H., Sakamoto M., Benno Y. Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation. Microbiol Immunol. 2002;46:819–831. doi: 10.1111/j.1348-0421.2002.tb02769.x. [DOI] [PubMed] [Google Scholar]
  15. Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010;464:908–912. doi: 10.1038/nature08937. [DOI] [PubMed] [Google Scholar]
  16. Hold G.L., Pryde S.E., Russell V.J., Furrie E., Flint H.J. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol. 2002;39:33–39. doi: 10.1111/j.1574-6941.2002.tb00904.x. [DOI] [PubMed] [Google Scholar]
  17. Hooper L.V., Gordon J.I. Commensal host-bacterial relationships in the gut. Science. 2001;292:1115–1118. doi: 10.1126/science.1058709. [DOI] [PubMed] [Google Scholar]
  18. Ivanov I.I., Atarashi K., Manel N., Brodie E.L., Shima T., Karaoz U., Wei D., Goldfarb K.C., Santee C.A., Lynch S.V., Tanoue T., Imaoka A., Itoh K., Takeda K., Umesaki Y., Honda K., Littman D.R. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139:485–498. doi: 10.1016/j.cell.2009.09.033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ivanov I.I., Frutos Rde L., Manel N., Yoshinaga K., Rifkin D.B., Sartor R.B., Finlay B.B., Littman D.R. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe. 2008;4:337–349. doi: 10.1016/j.chom.2008.09.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kitahara M., Sakamoto M., Ike M., Sakata S., Benno Y. Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 2005;55:2143–2147. doi: 10.1099/ijs.0.63788-0. [DOI] [PubMed] [Google Scholar]
  21. Kurokawa K., Itoh T., Kuwahara T., Oshima K., Toh H., Toyoda A., Takami H., Morita H., Sharma V.K., Srivastava T.P., et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14:169–181. doi: 10.1093/dnares/dsm018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Langendijk P.S., Schut F., Jansen G.J., Raangs G.C., Kamphuis G.R., Wilkinson M.H.F., Welling G.W. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. With genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol. 1995;61:3069–3075. doi: 10.1128/aem.61.8.3069-3075.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lederberg J., McCray A.T. ’Ome Sweet’ Omics—a genealogical treasury of words. The Scientist. 2001;15:8. [Google Scholar]
  24. Ley R.E., Peterson D.A., Gordon J.I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–848. doi: 10.1016/j.cell.2006.02.017. [DOI] [PubMed] [Google Scholar]
  25. Macfarlane G.T., Macfarlane S. Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut. Curr Opin Biotechnol. 2007;18:156–162. doi: 10.1016/j.copbio.2007.01.011. [DOI] [PubMed] [Google Scholar]
  26. Macfarlane G.T., Gibson G.R., Cummings J.H. Comparison of fermentation reactions in different regions of the human colon. J Appl Bacterial. 1992;72:57–64. doi: 10.1111/j.1365-2672.1992.tb05187.x. [DOI] [PubMed] [Google Scholar]
  27. Macfarlane G.T., Macfarlane S., Gibson G.R. Use of a three stage compound continuous culture systems to investigate bacterial growth and metabolism in the human colonic microbiota. Microb Ecol. 1998;35:180–187. doi: 10.1007/s002489900072. [DOI] [PubMed] [Google Scholar]
  28. Martinon F., Tschopp J.T. NLRs join TLRs as innate sensors of pathogens. Trends Immunol. 2005;26:447–454. doi: 10.1016/j.it.2005.06.004. [DOI] [PubMed] [Google Scholar]
  29. Michelsen K.S., Aicher A., Mohaupt M., Hartung T., Dimmeler S., Kirschning C.J., Schumann R.R. The role of toll-like receptors (TLRs) in bacteria-induced maturation of murine dendritic cells (DCS). Peptidoglycan and lipoteichoic acid are inducers of DC maturation and require TLR2. J Biol Chem. 2001;276:25680–25686. doi: 10.1074/jbc.M011615200. [DOI] [PubMed] [Google Scholar]
  30. Nichols D., Cahoon N., Trakhtenberg E.M., Pham L., Mehta A., Belanger A., Kanigan T., Lewis K., Epstein S.S. Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol. 2010;76:2445–2450. doi: 10.1128/AEM.01754-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Palframan R.J., Gibson G.R., Rastall R.A. Effect of pH and dose on the growth of gut bacteria on prebiotic carbohydrates in vitro. Anaerobe. 2002;8:287–292. doi: 10.1006/anae.2002.0434. [DOI] [PubMed] [Google Scholar]
  32. Peterson J., Garges S., Giovanni M., McInnes P., Wang L., Schloss J.A., Bonazzi V., McEwen J.E., Wetterstrand K.A., Deal C., the NIH HMP Working Group et al. The NIH Human Microbiome Project. Genome Res. 2009;19:2317–2323. doi: 10.1101/gr.096651.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., the MetaHIT Consortium et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65. doi: 10.1038/nature08821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Relman D.A. New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J Infect Dis. 2002;186:S254–S258. doi: 10.1086/344935. [DOI] [PubMed] [Google Scholar]
  35. Relman D.A., Falkow S. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 2001;9:206–208. doi: 10.1016/S0966-842X(01)02041-8. [DOI] [PubMed] [Google Scholar]
  36. Savage D.C. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107–133. doi: 10.1146/annurev.mi.31.100177.000543. [DOI] [PubMed] [Google Scholar]
  37. Suau A., Bonnet R., Sutren M., Godon J.J., Gibson G.R., Collins M.D., Doré J. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol. 1999;65:4799–4807. doi: 10.1128/aem.65.11.4799-4807.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Tap J., Mondot S., Levenez F., Pelletier E., Caron C., Furet J.P., Ugarte E., Muñoz-Tamayo R., Paslier D.L., Nalin R., et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009;11:2574–2584. doi: 10.1111/j.1462-2920.2009.01982.x. [DOI] [PubMed] [Google Scholar]
  39. Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., Gordon J.I. The human microbiome project. Nature. 2007;449:804–810. doi: 10.1038/nature06244. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–484. doi: 10.1038/nature07540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Umesaki Y., Okada Y., Matsumoto S., Imaoka A., Setoyama H. Segmented filamentous bacteria are indigenous intestinal bacteria that activate intraepithelial lymphocytes and induce MHC class II molecules and fucosyl asialo GM1 glycolipids on the small intestinal epithelial cells in the ex-germ-free mouse. Microbiol Immunol. 1995;39:555–562. doi: 10.1111/j.1348-0421.1995.tb02242.x. [DOI] [PubMed] [Google Scholar]
  42. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74. doi: 10.1126/science.1093857. [DOI] [PubMed] [Google Scholar]
  43. Wang X., Gibson G.R. Effects of the in vitro fermentation of oligofructose and inulin by bacteria growing in the human large intestine. J Appl Bacteriol. 1993;75:373–380. doi: 10.1111/j.1365-2672.1993.tb02790.x. [DOI] [PubMed] [Google Scholar]
  44. Wang X., Heazlewood S.P., Krause D.O., Florin T.H. Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J Appl Microbiol. 2003;95:508–520. doi: 10.1046/j.1365-2672.2003.02005.x. [DOI] [PubMed] [Google Scholar]
  45. Winitz M., Adams R.F., Seedman D.A., Davis P.N., Jayko L.G., Hamilton J.A. Studies in metabolic nutrition employing chemically defined diets. II. Effects on gut microflora populations. Am J Clin Nutr. 1970;23:546–559. doi: 10.1093/ajcn/23.5.546. [DOI] [PubMed] [Google Scholar]
  46. Yamauchi K.E., Snel J. Transmission electron microscopic demonstration of phagocytosis and intracellular processing of segmented filamentous bacteria by intestinal epithelial cells of the chick ileum. Infect Immun. 2000;68:6496–6504. doi: 10.1128/IAI.68.11.6496-6504.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yin Y., Lei F., Zhu L., Li S., Wu Z., Zhang R., Gao G.F., Zhu B., Wang X. Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression. ISME J. 2010;4:367–376. doi: 10.1038/ismej.2009.128. [DOI] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES