Protein & Cell

, Volume 1, Issue 8, pp 718–725 | Cite as

Human gut microbiome: the second genome of human body

  • Baoli ZhuEmail author
  • Xin Wang
  • Lanjuan Li


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.


Human Microbiome Project Human Microbiota Core Microbiome Human Intestinal Microbiota Functional Gene Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ahmed, S., Macfarlane, G.T., Fite, A., McBain, A.J., Gilbert, P., and Macfarlane, S. (2007). Mucosa-Associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol 73, 7435–7442.CrossRefGoogle Scholar
  2. Aoi, Y., Kinoshita, T., Hata, T., Ohta, H., Obokata, H., and Tsuneda, S. (2009). Hollow-fiber membrane chamber as a device for in situ environmental cultivation. Appl Environ Microbiol 75, 3826–3833.CrossRefGoogle Scholar
  3. Bäckhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and Gordon, J.I. (2005). Host-bacterial mutualism in the human intestine. Science 307, 1915–1920.CrossRefGoogle Scholar
  4. Bollmann, A., Lewis, K., and Epstein, S.S. (2007). Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates. Appl Environ Microbiol 73, 6386–6390.CrossRefGoogle Scholar
  5. Child, M.W., Kennedy, A., Walker, A.W., Bahrami, B., Macfarlane, S., and Macfarlane, G.T. (2006). 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 55, 299–310.CrossRefGoogle Scholar
  6. Davies, J. (2001). In a map for human life, count the microbes, too. Science 291, 2316.CrossRefGoogle Scholar
  7. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., and Relman, D.A. (2005). Diversity of the human intestinal microbial flora. Science 308, 1635–1638.CrossRefGoogle 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. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31, 677–689.CrossRefGoogle Scholar
  9. Gibson, G.R., and Wang, X. (1994). Enrichment of bifidobacteria from human gut contents by oligofructose using continuous culture. FEMS Microbiol Lett 118, 121–127.CrossRefGoogle 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., and Nelson, K.E. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359.CrossRefGoogle Scholar
  11. Haller, D., Jobin, C. (2004). Interaction between resident luminal bacteria and the host: can a healthy relationship turn sour? J Pediatr Gastroenterol Nutr 38, 123–136.CrossRefGoogle Scholar
  12. Handelsman, J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68, 669–685.CrossRefGoogle Scholar
  13. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., and Goodman, R.M. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5, R245–R249.CrossRefGoogle Scholar
  14. Hayashi, H., Sakamoto, M., and Benno, Y. (2002). Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation. Microbiol Immunol 46, 819–831.CrossRefGoogle Scholar
  15. Hehemann, J.H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., and Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912.CrossRefGoogle Scholar
  16. Hold, G.L., Pryde, S.E., Russell, V.J., Furrie, E., and Flint, H.J. (2002). Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 39, 33–39.CrossRefGoogle Scholar
  17. Hooper, L.V., and Gordon, J.I. (2001). Commensal host-bacterial relationships in the gut. Science 292, 1115–1118.CrossRefGoogle Scholar
  18. Ivanov, II., 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. (2009). Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498.CrossRefGoogle Scholar
  19. Ivanov, II., Frutos Rde, L., Manel, N., Yoshinaga, K., Rifkin, D.B., Sartor, R.B., Finlay, B.B., Littman, D.R. (2008). Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4, 337–349.CrossRefGoogle Scholar
  20. Kitahara, M., Sakamoto, M., Ike, M., Sakata, S., and Benno, Y. (2005). Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 55, 2143–2147.CrossRefGoogle 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. (2007). Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14, 169–181.CrossRefGoogle Scholar
  22. Langendijk, P.S., Schut, F., Jansen, G.J., Raangs, G.C., Kamphuis, G.R., Wilkinson, M.H.F., and Welling, G.W. (1995). Quantitative fluorescence in situ hybridization of Bifidobacterium spp. With genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol 61, 3069–3075.Google Scholar
  23. Lederberg, J., and McCray, A.T. (2001). ’Ome Sweet’ Omics—a genealogical treasury of words. The Scientist 15, 8.Google Scholar
  24. Ley, R.E., Peterson, D.A., and Gordon, J.I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837–848.CrossRefGoogle Scholar
  25. Macfarlane, G.T., and Macfarlane, S. (2007). Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut. Curr Opin Biotechnol 18, 156–162.CrossRefGoogle Scholar
  26. Macfarlane, G.T., Gibson, G.R., and Cummings, J.H. (1992). Comparison of fermentation reactions in different regions of the human colon. J Appl Bacterial 72, 57–64.CrossRefGoogle Scholar
  27. Macfarlane, G.T., Macfarlane, S., and Gibson, G.R. (1998). Use of a three stage compound continuous culture systems to investigate bacterial growth and metabolism in the human colonic microbiota. Microb Ecol 35, 180–187.CrossRefGoogle Scholar
  28. Martinon, F., and Tschopp, J.T. (2005). NLRs join TLRs as innate sensors of pathogens. Trends Immunol 26, 447–454.CrossRefGoogle Scholar
  29. Michelsen, K.S., Aicher, A., Mohaupt, M., Hartung, T., Dimmeler, S., Kirschning, C.J., and Schumann, R.R. (2001). 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 276, 25680–25686.CrossRefGoogle Scholar
  30. Nichols, D., Cahoon, N., Trakhtenberg, E.M., Pham, L., Mehta, A., Belanger, A., Kanigan, T., Lewis, K., and Epstein, S.S. (2010). Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol 76, 2445–2450.CrossRefGoogle Scholar
  31. Palframan, R.J., Gibson, G.R., and Rastall, R.A. (2002). Effect of pH and dose on the growth of gut bacteria on prebiotic carbohydrates in vitro. Anaerobe 8, 287–292.CrossRefGoogle 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., et al., and the NIH HMP Working Group. (2009). The NIH Human Microbiome Project. Genome Res 19, 2317–2323.CrossRefGoogle Scholar
  33. Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al., and the MetaHIT Consortium. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.CrossRefGoogle Scholar
  34. Relman, D.A. (2002). New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J Infect Dis 186, S254–S258.CrossRefGoogle Scholar
  35. Relman, D.A., and Falkow, S. (2001). The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 9, 206–208.CrossRefGoogle Scholar
  36. Savage, D.C. (1977). Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31, 107–133.CrossRefGoogle Scholar
  37. Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D., and Doré, J. (1999). Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65, 4799–4807.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. (2009). Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11, 2574–2584.CrossRefGoogle Scholar
  39. Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. (2007). The human microbiome project. Nature 449, 804–810.CrossRefGoogle 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. (2009). A core gut microbiome in obese and lean twins. Nature 457, 480–484.CrossRefGoogle Scholar
  41. Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A., Setoyama, H. (1995). 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 39, 555–562.CrossRefGoogle 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. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74.CrossRefGoogle Scholar
  43. Wang, X., Gibson, G.R. (1993). Effects of the in vitro fermentation of oligofructose and inulin by bacteria growing in the human large intestine. J Appl Bacteriol 75, 373–380.CrossRefGoogle Scholar
  44. Wang, X., Heazlewood, S.P., Krause, D.O., and Florin, T.H. (2003). Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J Appl Microbiol 95, 508–520.CrossRefGoogle Scholar
  45. Winitz, M., Adams, R.F., Seedman, D.A., Davis, P.N., Jayko, L.G., and Hamilton, J.A. (1970). Studies in metabolic nutrition employing chemically defined diets. II. Effects on gut microflora populations. Am J Clin Nutr 23, 546–559.Google Scholar
  46. Yamauchi, K.E., Snel, J. (2000). Transmission electron microscopic demonstration of phagocytosis and intracellular processing of segmented filamentous bacteria by intestinal epithelial cells of the chick ileum. Infect Immun 68, 6496–6504.CrossRefGoogle Scholar
  47. Yin, Y., Lei, F., Zhu, L., Li, S., Wu, Z., Zhang, R., Gao, G.F., Zhu, B., Wang, X. (2010). Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression. ISME J 4, 367–376.CrossRefGoogle Scholar

Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
  2. 2.Institute of Plant Protection and MicrobiologyZhejiang Academy of Agricultural SciencesHangzhouChina
  3. 3.State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of MedicineZhejiang UniversityHangzhouChina

Personalised recommendations