Gut flora

community of microorganisms in the digestive tracts of humans

Gut flora consists of microorganisms that live in the digestive system of animals. It is the largest reservoir of microbes in the human microbiome.

Escherichia coli, one of the many species of bacteria present in the human gut

The human body, consisting of about 100 trillion cells, carries about ten times as many microorganisms in the intestines.[1][2][3][4] The metabolic activities performed by these bacteria resemble those of an organ, leading some to call gut flora a 'forgotten organ'.[5] It is estimated that these gut flora have around 100 times as many genes in aggregate as there are in the human genome.[6]

Bacteria make up most of the flora in the colon[7] and up to 60% of the dry mass of faeces.[2] Somewhere between 300[2] and 1000 different species live in the gut,[3] with most estimates at about 500.[4][5][8] However, it is probable that 99% of the bacteria come from about 30 or 40 species.[9] Fungi and protozoa also make up a part of the gut flora, but little is known about their activities.

Research suggests that the relationship between gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a symbiotic relationship.[3] Though people can survive without gut flora,[4] the microorganisms perform a lot of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful, pathogenic bacteria,[2] regulating the development of the gut, producing vitamins for the host (such as biotin and vitamin K), and producing hormones to direct the host to store fats. However, in some conditions, some species can cause disease by producing an infection or increasing cancer risk for the host.[2][7]

Such food compounds as polyphenols, oligosaccharides and polysaccharides may be useful for good bacteria and help reduce pathogenic species of human gut flora.[10]

Over 99% of the bacteria in the gut are anaerobic,[2][3][7][9][11] but in the cecum, aerobic bacteria reach high densities.[2]

The traditional view is that no metazoan phylum can break down cellulose by producing the enzyme cellulase. Instead, herbivores contain, in their gut, microorganisms which produce cellulase.[12][13] This is important because cellulose is the most common organic compound on Earth. About 33% of all plant matter is cellulose (the cellulose content of cotton is 90% and that of wood is 40–50%).[14] Recently, evidence has emerged that some animals do produce their own cellulase.[15] The question is not yet quite settled.[16]



  1. Björkstén B, Sepp E, Julge K, Voor T, Mikelsaar M (October 2001). "Allergy development and the intestinal microflora during the first year of life". J. Allergy Clin. Immunol. 108 (4): 516–20. doi:10.1067/mai.2001.118130. PMID 11590374.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Guarner F, Malagelada JR (February 2003). "Gut flora in health and disease". Lancet. 361 (9356): 512–9. doi:10.1016/S0140-6736(03)12489-0. PMID 12583961. S2CID 38767655.
  3. 3.0 3.1 3.2 3.3 Sears CL (October 2005). "A dynamic partnership: celebrating our gut flora". Anaerobe. 11 (5): 247–51. doi:10.1016/j.anaerobe.2005.05.001. PMID 16701579.
  4. 4.0 4.1 4.2 Steinhoff U (June 2005). "Who controls the crowd? New findings and old questions about the intestinal microflora". Immunol. Lett. 99 (1): 12–6. doi:10.1016/j.imlet.2004.12.013. PMID 15894105.
  5. 5.0 5.1 O'Hara A.M. & Shanahan F. 2006. The gut flora as a forgotten organ. EMBO Report 7: 688–93. PMID 16819463.
  6. Junjie Qin; et al. (2009). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
  7. 7.0 7.1 7.2 University of Glasgow. 2005. The normal gut flora. Available through web archive. Accessed May 22, 2008
  8. Gibson RG (2004). "Fibre and effects on probiotics (the prebiotic concept)". Clinical Nutrition Supplements. 1 (2): 25–31. doi:10.1016/j.clnu.2004.09.005.
  9. 9.0 9.1 Beaugerie L, Petit JC (April 2004). "Microbial-gut interactions in health and disease. Antibiotic-associated diarrhoea". Best Pract Res Clin Gastroenterol. 18 (2): 337–52. doi:10.1016/j.bpg.2003.10.002. PMID 15123074.
  10. Hoda M. Eid. | display-authors = etal Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients
  11. Vedantam G, Hecht DW (October 2003). "Antibiotics and anaerobes of gut origin". Curr. Opin. Microbiol. 6 (5): 457–61. doi:10.1016/j.mib.2003.09.006. PMID 14572537.
  12. Cleveland L.R. 1923. Symbiosis between termites and their intestinal protozoa. Proc Natl Acad Sci U S A 9(12): 424–428.
  13. Hobson P.N; & Stewart C.S. 1997. The rumen microbial ecosystem. 2nd ed, Springer, New York. ISBN 0-7514-0366-0.
  14. "Chemical Composition of Wood" (PDF). Archived from the original (PDF) on 2011-01-03. Retrieved 2011-06-03.
  15. Watanabe H, Tokuda G (2001). "Animal cellulases". Cell. Mol. Life Sci. 58 (9): 1167–1178. doi:10.1007/PL00000931. PMID 11577976. S2CID 570164.
  16. Tokuda, G; Watanabe, H (2007). "Hidden cellulases in termites: revision of an old hypothesis". Biology Letters. 3 (3): 336–339. doi:10.1098/rsbl.2007.0073. PMC 2464699. PMID 17374589.