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The human flora is the assemblage of microorganisms that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, and in the gastrointestinal tracts. They include bacteria, fungi and archaea. Some of these organisms are known to perform tasks that are useful for the human host, while the majority have no known beneficial or harmful effect. Those that are expected to be present, and that under normal circumstances do not cause disease, but instead participate in maintaining health, are deemed members of the normal flora,[1] or microbiota. An effort to better describe the microflora of humans has been initiated; see Human microbiome project.

Though widely known as "microflora", this is technically a misnomer since the word root "flora" pertains to plants and biota refers to the total collection of organisms in a particular ecosystem. Thus recently, the more appropriate term "microbiota" is applied, though its use has not eclipsed the entrenched use and recognition of "flora" with regard to bacteria and other microorganisms. Both terms are being used in different textbooks.

Studies in 2009 questioned whether the decline in biota (including microfauna) as a result of human intervention might impede human health[2]


Bacterial flora


Culturable and nonculturable bacteria

Traditionally, bacteria have been described by how they grow - what they grow on, color of the colony and so forth. More recently, bacteria have been described on the basis of DNA sequencing. One common finding is that the number of bacteria - both in terms of diversity (number of different types) and mass (total number of cells) is very different when a surface is sampled for culturable bacteria or sampled for DNA. DNA evidence suggests that well described species - in essence, species that can be cultured - constitute <10% of the total bacterial population seen with DNA based techniques; that is, most of the bacteria present on the human skin or in the gut are species known only by their DNA, and, are species that until very recently were completely unknown to science.

It is estimated that 500 to 1000 species of bacteria live in the human gut[3] and a roughly similar number on the skin.[4][5] Bacterial cells are much smaller than human cells, and there are at least ten times as many bacteria as human cells in the body (approximately 1014 versus 1013).[6][7] Though members of the flora are found on all surfaces exposed to the environment (on the skin and eyes, in the mouth, nose, small intestine), the vast majority of bacteria live in the large intestine.

Many of the bacteria in the digestive tract, collectively referred to as the gut flora, are able to break down certain nutrients such as carbohydrates that humans otherwise could not digest. The majority of these commensal bacteria are anaerobes, meaning they survive in an environment with no oxygen. Bacteria of the normal flora can act as opportunistic pathogens at times of lowered immunity.[1]

Escherichia coli (a.k.a. E. coli) is a bacterium that lives in the colon; it is an extensively studied model organism and probably the best understood bacterium of all.[8] Certain mutated strains of these gut bacteria do cause disease; an example is E. coli O157:H7.

A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the mouth, where they are part of a sticky substance called plaque. If this is not removed by brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that dissolve tooth enamel, causing tooth decay.

The vaginal microflora consist mostly of various lactobacillus species. It was long thought that the most common of these species was Lactobacillus acidophilus, but it has later been shown that the most common one is L. iners followed by L. crispatus. Other lactobacilli found in the vagina are L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to bacterial vaginosis.

Archaean flora

Archaea are present in the human gut, but in contrast to the enormous variety of bacteria in this organ, the number of archaeal species are much more limited.[9] The dominant group are the methanogens, particularly Methanobrevibacter smithii and Methanosphaera stadtmanae.[10] However, colonization by methanogens is variable and only about 50% of humans have easily-detectable populations of these organisms.[11]

No apparent effect on health

As of 2007, no clear examples of archaeal pathogens are known,[12][13] although a relationship has been proposed between the presence of some methanogens and human periodontal disease.[14]

Fungal flora

Fungi, particularly yeasts are present in the human gut. The best studied of these are Candida species. This is because of their ability to become pathogenic in immunocompromised hosts.[15] Yeasts are also present on the skin, particularly Malassezia species, where they consume oils secreted from the sebaceous glands.[16][17]

Flora by anatomical area

Skin flora

A study of 20 skin sites on each of 10 healthy humans found 205 identified genera in nineteen bacterial phyla, with most sequences assigned to four phyla: Actinobacteria (51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%)[18].

Nasal flora

Gut flora

The gut flora is the human flora of microorganisms that normally live in the digestive tract and can perform a number of useful functions for their hosts. The average human body, consisting of about 1013 (10,000,000,000,000 or about ten trillion) cells, has about ten times that number of microorganisms in the gut.[19][20][21][22] There's an estimate of about 500 different bacterial species in the intestine.[23] The metabolic activity performed by these bacteria is equal to that of a virtual organ making the gut bacteria termed as a "forgotten" organ.[23]

Bacteria make up most of the flora in the colon[24] and 60% of the dry mass of feces.[21] This fact makes feces an ideal source to test for gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens, and bacterial 16S rRNA gene sequences are generated with bacterial primers. This form of testing is also often preferable to more invasive techniques, such as biopsies. Somewhere between 300[21] and 1000 different species live in the gut,[19] with most estimates at about 500.[22][25] However, it is probable that 99% of the bacteria come from about 30 or 40 species.[26] 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[27] and humans is not merely commensal (a non-harmful coexistence), but rather is a mutualistic, symbiotic relationship.[19] Though people can survive with no gut flora,[22] the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system, preventing growth of harmful species,[21] 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 certain conditions, some species are thought to be capable of causing disease by causing infection or increasing cancer risk for the host.[21][24]

Vaginal flora

Oral cavity

See also


  1. ^ a b Samuel Baron MD; Charles Patrick. Davis (1996). Bacteriology. University of Texas Medical Branch at Galveston. pp. Chapter 6. Normal Flora. 
  2. ^ Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear?, Katherine Harmon, scientific American, 16 December 2009, accessed 27 December 2009
  3. ^ Sears CL (2005). "A dynamic partnership: celebrating our gut flora". Anaerobe (Academic Press) (5):247-51 (5): 247–251. doi:10.1016/j.anaerobe.2005.05.001. PMID 16701579. 
  4. ^ Grice EA, Kong HH, Conlan S. (2009). Topographical and Temporal Diversity of the Human Skin Microbiome, Science, 324: 1190 - 1192. doi:10.1126/science.1171700
  5. ^ Pappas S. (2009). Your Body Is a habitat ... for Bacteria. Science Now Daily News
  6. ^ Savage, D. C. (1977). "Microbial Ecology of the Gastrointestinal Tract". Annual Review of Microbiology 31: 107. doi:10.1146/annurev.mi.31.100177.000543. PMID 334036. 
  7. ^ Berg, R. (1996). "The indigenous gastrointestinal microflora". Trends in Microbiology 4 (11): 430. doi:10.1016/0966-842X(96)10057-3. PMID 8950812. 
  8. ^ Lee PS, Lee KH (2003). "Escherichia coli--a model system that benefits from and contributes to the evolution of proteomics.". Biotechnol Bioeng 84 (7): 801–14. doi:10.1002/bit.10848. PMID 14708121. 
  9. ^ Eckburg PB, Bik EM, Bernstein CN, et al. (2005). "Diversity of the human intestinal microbial flora". Science 308 (5728): 1635–8. doi:10.1126/science.1110591. PMID 15831718. 
  10. ^ Duncan SH, Louis P, Flint HJ (2007). "Cultivable bacterial diversity from the human colon". Lett. Appl. Microbiol. 44 (4): 343–50. doi:10.1111/j.1472-765X.2007.02129.x. PMID 17397470. 
  11. ^ Florin TH, Zhu G, Kirk KM, Martin NG (2000). "Shared and unique environmental factors determine the ecology of methanogens in humans and rats". Am. J. Gastroenterol. 95 (10): 2872–9. doi:10.1111/j.1572-0241.2000.02319.x. PMID 11051362. 
  12. ^ Eckburg P, Lepp P, Relman D (2003). "Archaea and their potential role in human disease". Infect Immun 71 (2): 591–6. doi:10.1128/IAI.71.2.591-596.2003. PMID 12540534. 
  13. ^ Cavicchioli R, Curmi P, Saunders N, Thomas T (2003). "Pathogenic archaea: do they exist?". Bioessays 25 (11): 1119–28. doi:10.1002/bies.10354. PMID 14579252. 
  14. ^ Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D (2004). "Methanogenic Archaea and human periodontal disease". Proc Natl Acad Sci USA 101 (16): 6176–81. doi:10.1073/pnas.0308766101. PMID 15067114. 
  15. ^ Bernhardt H, Knoke M (1997). "Mycological aspects of gastrointestinal microflora". Scand. J. Gastroenterol. Suppl. 222: 102–6. PMID 9145460. 
  16. ^ Marcon MJ, Powell DA (1 April 1992). "Human infections due to Malassezia spp". Clin. Microbiol. Rev. 5 (2): 101–19. PMID 1576583.& PMC 358230. 
  17. ^ Roth RR, James WD (1988). "Microbial ecology of the skin". Annu. Rev. Microbiol. 42: 441–64. doi:10.1146/annurev.mi.42.100188.002301. PMID 3144238. 
  18. ^ Elizabeth A. Grice et al. (2006). "Topographical and Temporal Diversity of the Human Skin Microbiome". Science 324 (5931): 1190–2. doi:10.1126/science.1171700.
  19. ^ a b c Sears CL. 2005. A dynamic partnership: Celebrating our gut flora. Anaerobe, Volume 11, Issue 5, Pages 247-251. PMID 16701579.
  20. ^ Björkstén B, Sepp E, Julge K, Voor T, and Mikelsaar and M. 2001. Allergy development and the intestinal microflora during the first year of life. Journal of Allergy and Clinical Immunology, Volume 108, Issue 4, Pages 516-520. PMID 11590374.
  21. ^ a b c d e Guarner F and Malagelada JR. 2003. Gut flora in health and disease. The Lancet, Volume 361, Issue 9356, 8 February 2003, Pages 512-519. PMID 12583961.
  22. ^ a b c Steinhoff U. 2005. Who controls the crowd? New findings and old questions about the intestinal microflora. Immunology Letters, Volume 99, Issue 1, June , Pages 12-16. PMID 15894105. doi:10.1016/j.imlet.2004.12.013
  23. ^ a b Ann M O'Hara, Fergus Shanahan The gut flora as a forgotten organ. EMBO reports 7, 688 - 693 (01 Jul 2006)
  24. ^ a b University of Glasgow. 2005. The normal gut flora. Available through web archive. Accessed May 22, 2008
  25. ^ Gibson RG. 2004. Fibre and effects on probiotics (the prebiotic concept). Clinical Nutrition Supplements, Volume 1, Issue 2, Pages 25-31.
  26. ^ Beaugerie L and Petit JC. 2004. Microbial-gut interactions in health and disease. Antibiotic-associated diarrhoea. Best Practice & Research Clinical Gastroenterology, Volume 18, Issue 2, Pages 337-352. PMID 15123074.
  27. ^ Gut flora are also known as gut microbiota.


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