Human microbiota

The human microbiota comprises of the aggregate of microorganisms, which colonize various parts of the body. Microbiological studies have found that different groups of microorganisms perform exactly the same metabolic processes in each individual. 1

The indigenous group of organisms normally present at a particular given anatomical site is known as indigenous microbiota. 2

Certain areas of the body are more densely colonized by microorganisms than others. This phenomenon is known as ‘tissue specificity’. The reasons for tissue specificity are " 2

1. Tissue tropism " Availability of specific nutrients and optimal conditions for survival in certain parts of the body encourages microorganisms to colonize and establish microbiota in that region

2. Specific adherence " The microbial cell contains certain components known as ligands or adhesion components which help in binding with microbial cell receptors.

3. Biofilm formation " Biofilm is the adherence of microorganisms to a cellular surface and in turn to one another so as to form a film or layer of colonized microorganisms, and enclosed within a matrix of extracellular polymeric substance (EPS). 3

Before birth, the foetus exists in a completely sterile environment. However, the processes of parturition as well as lactation mean that microbiota get transferred on to the neonatal system, and microbial colonization begins. This results in the establishment of normal or indigenous microbiota in the neonatal system in a period of about 48 hours. 2

What is mutualism?

Symbiosis is the close and long-term association of two or more organisms, which can be " 4

- Parasitism " The parasite derives its nutritional benefits from the host organism.

- Commensalism " One organism benefits and other organism is unaffected by this association

- Mutualism " A mutually beneficial association

Mutualistic association of microbiota in each part of the body is as follows

- Scalp " Fungi are normally found on the human scalp. This is known as Mycobiome. Normally occurring fungi provide protection to the scalp against pathogenic infections. 5 In turn, the fungi utilize the conditions in the scalp for their own growth and survival. In a healthy scalp, fungal species of Coniochaeta, Cryptococcus (non-pathogenic), Didymella, Rhodotorula, have been found in greater frequencies. 6

- Skin " Normal skin microbiota have been thought to be commensal until now. However, emerging evidence states that bacteria present on the surface of the skin may in fact be associated with host defence mechanism. For example, Gram positive Staphylococcus epidermidis as well as other mutuals. However, it is to be noted that the same bacteria ma transform from mutual to commensal to parasitic depending upon the environmental conditions. It has been found that strains of S. epidermidis produce lantibiotics or bacteriocins (lanthionine containing anti-bacterial peptides). These peptides have been found to display toxic effects against pathogenic microorganisms such as Staphylococcus aureus and Group A Streptococcus (GAS). The presence of S. epidermidis also encourages the production of the body’s own immune responses (antimicrobial molecules). Conversely, usage of topic antibiotics may eliminate presence of S. epidermidis from the skin surface which may have an adverse impact on the host immune responses. 7

Pseudomonas aeruginosa is an opportunistic microorganism which can display skin protective effects. It produces pseudomonic acid (an antimicrobial component) that works against infections caused by staphylococcal and streptococcal organisms. It also displays antimicrobial activity against Candida krusei, Candida albicans, Torulopsis glabrata, Saccharomyces cerevisiae, and Aspergillus fumigatus. 8

- Oral cavity " Over 700 species of microorganisms have been identified in healthy oral cavity. Some of the species are - Streptococcus, Actinomyces, Veillonella, Fusobacterium, Porphromonas, Prevotella, Treponema, Nisseria, Haemophilis, Eubacteria, Lactobacterium, Capnocytophaga, Eikenella, Leptotrichia, Peptostreptococcus, Staphylococcus , and Propionibacterium. These bacteria maintain a mutualistic association with the host organism. They do not allow pathogens to adhere to surfaces inside the oral cavity, thereby preventing biofilm formation and infection. 9

- Gut " The gastrointestinal tract comprises of upto 1000 species of bacteria. 10 Gut microorganisms perform a variety of functions in the human body " 11,12,13,14,15

  • Digestion of food " Bacteria such as Lactobacillus and Bifidobacterium help ferment indigestible carbohydrates (producing lactic acid) as well as break down lactose-containing food products into simpler sugars. Production of lactic acid in turn helps in the proper absorption of micronutrients such as calcium, copper, etc., as well as the release of digestive juices and enzymes, thus enabling proper functioning of the digestive glands. 16
  • Productions of vitamins " Humans do not possess the ability to synthesize vitamins on their own. Gut bacteria assist in the production of vitamin B complex 17 , as well as vitamin K2 18.
  • Maintenance of intestinal mucosa " It has been found that consumption of diet rich in Baker’s yeast has a favourable effect on the integrity of intestinal mucosa. 19 The main functions of the intestinal mucosa include absorption of digestion products, as well as secretion of bicarbonate ions which neutralize the acidic contents in the digestive chyme. 20
  • Suppression of pathogenic microbial growth " Gut microbiota protects the host organism against pathogenic colonization as well as preventing disruption of the indigenous gut microbial community. The mechanisms involved to carry out these functions include metabolic interactions, specificity to intestine, as well as host immune reactions. For example, mutualistic E. coli produces a bacteriocin that inhibits the growth of pathogenic E. coli (enterohaemorrhagic E. coli). Gut microbiota also generate short-chain fatty acids which alter pH of the gut, preventing the colonization of pathogenic microorganisms. 21
  • Immunity " Interaction between the host immune system as well as microorganisms takes place in the gut. Intestinal microbiota support the immune and metabolic functions in the host organism. Gut microbiota form an integral component of the innate immune system as they can distinguish between pathogenic and non-pathogenic microorganisms. 22
  • Metabolism " Methanogenic archaebacteria (Methanobrevibacter smithii) are involved in the removal of end products of fermentation. Gut microflora also metabolize vitamins, and help in the absorption of magnesium, calcium, etc. 23
  • Allergy prevention " Research studies have found that a mix of Clostridia (native to gut) have been found to protect against food allergies by inducing those immune responses which block specific allergens from entering the bloodstream, thus preventing an allergic response from the host organism. 24
  • Prevention of bowel disorders " Overuse of antibiotics disrupts the normal indigenous constitution of gut flora present in an individual. This leads to increased susceptibility to bowel disorders such as irritable bowel syndrome (IBS). 25
  • Maintenance of body weight " The presence of bacteria belonging to the family Christensenellaceae plays a crucial role in the maintenance of body weight. These bacteria form a network with methanogenic bacteria. These bacteria were found in greater amount in individuals having low BMI. 26
- Genitourinary tract " Vaginal microbiota is regarded to be healthy when hydrogen peroxide producing microorganisms inhabit it. For example,Lactobacillus crispatus and Lactobacillus jensenii. 27 They colonize the vagina and prevent bacterial vaginosis. 28 Lactobacillus acidophilus is present in the vagina during fertility and decreases the vaginal pH, preventing pathogenic infection. 2

Microbiota existence has been found in other parts of the body such as the conjunctiva, and the respiratory tract. However, no mutualistic association has been exhibited by microorganisms present in these parts.


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27. Martin DH, Zozaya M, Lillis R, Miller J, Ferris MJ. The Microbiota of the Human Genitourinary Tract: Trying to See the Forest Through the Trees. Transactions of the American Clinical and Climatological Association. 2012;123:242-256

28. Lactobacillius crispatus " Wikipedia, The Free Encyclopedia. Available from (Accessed on June 2, 2016)

About Author / Additional Info:
I am a post-graduate in Biochemistry from the University of Mumbai