Distribution of Microflora in the Body

There are plethora of microorganisms in the intestinal tract of humans and other animals, and these organisms or normal floras play vital roles of protecting the intestines and its associated organs from invading pathogenic microorganisms. Some of the functions carried out by normal microflora in the gastrointestinal tract of humans include the repression of the growth of pathogens, digestion of un-utilized energy substrates, stimulation of cell growth, and training of the immune system to respond only to pathogens. The entire gastrointestinal tract (GIT) of humans is usually sterile (i.e., free from microorganisms) at birth, but different types of microbes (both harmful and beneficial) start to colonize the human gut following the intake of food.

Over 500 different species of microorganisms are found in the human gut, and the type of microorganisms that colonize each sections of the gastrointestinal tract varies greatly with the type of food eaten. For example, Bifidobacterium is the most prevalent bacterium or normal flora that occupies the GIT of infants on breast milk. Bifidobacterium is later joined by other microbes including Enterobacteriaceae, Lactobacillus, Bacteroides, Clostridium and Enterococci following the weaning of the infants. These microbes (especially Bifidobacteria) are known as normal microflora of the intestinal tract, and they play vital roles in the GIT including prevention of the colonization of the gut by pathogenic microorganisms (Table 1).

In addition, these organisms also help to improve digestion and nutrition in their human host, and a handful of them such as Bifidobacteria are known to produce important vitamins (e.g., vitamin B12 and K) in the body. However, bacterial related diseases and even mycoses can ensue when the natural balance of the normal microflora in the body is tempered with especially via prolonged antibiotic usage, malnutrition and the contraction of some diseases such as AIDS (Table 1). The main parts of the human body naturally colonized by harmless microorganisms (i.e., normal microflora) and the diseases that can ensue in those parts when the normal body functioning is destabilized are summarized in Table 1.

After exposure to an infectious agent, the body becomes contaminated by the agent, and the pathogenic microorganism eventually develops disease or infection in the susceptible human or animal host following a defined pattern (Figure 1). It is the duty of clinical microbiologists to isolate and characterize the infecting pathogenic microorganism(s), and differentiate same from normal microflora so that the appropriate treatment can be administered in order to restore the host to its normal working condition prior to its invasion by the pathogen.

Table 1: Some microbiota of the human body & their location




Pseudomonas, Enterobacteriaceae, coagulase-negative Staphylococci (CNS), Diphtheroids   Outer ear Otitis media, sepsis, bacteraemia & diphtheria
Streptococcus, Propionibacterium, staphylococcus, Pseudomonas, Acinetobacter, Klebsiella, Enterobacter, Corynebacterium, Malassezia, Proteus, Pityrosporum, Candida    Skin Bacteraemia, septicaemia, pneumonia, candidiasis    
Enterococci, Mycobacterium, Actinomyces, Bacteroides, Peptostreptococci, Escherichia, Fusobacterium, Proteus, Klebsiella, Lactobacillus, Clostridium, Pseudomonas, Acinetobacter, Streptococcus, Staphylococcus, CNS Large intestine  


Staphylococcal & streptococcal infections, septicaemia, bacteraemia

Streptococci, CNS, Haemophilus, Staphylococci Eye (conjunctiva) Conjunctivitis, bacteraemia, pneumonia 
Enterobacteriaceae, Lactobacilli, Clostridium, Enterococci, Mycobacterium, Bacteroides Small intestine Bacteraemia & sepsis
Streptococci, staphylococci, Eikenella, Candida, Veillonella, Streptococci Viridans, Fusobacterium, Neisseria, Corynebacterium,  Treponema, Actinomyces, CNS, Prevotella, Haemophilus, Capnocytophaga, Lactobacilli, Geotrichum Mouth and respiratory tract

Sore throat, sepsis, pneumonia, meningitis, candidiasis,  & bacteraemia

Fusobacterium, CNS, Peptostreptococci, Streptococci, Bacteroides, Mycobacterium Urethra Urethritis & sepsis
Helicobacter, Streptococci, Enterobacteriaceae, Staphylococci, Lactobacillus, Peptostreptococci Stomach Septicaemia & bacteraemia

 Neisseria, CNS, Haemophilus, Staphylococci, streptococci

Nose Upper respiratory tract infection
Clostridium, Candida, Lactobacilli, Gardnerella, Diphtheroids, Bacteroides, Streptococci, Peptostreptococci  Vagina

Vaginitis, candidiasis & urethritis

Figure 1: Flowchart of disease development in a host. This pathway shows the development of disease in the body after exposure to an infectious agent. MicroDok


Brooks G.F., Butel J.S and Morse S.A (2004). Medical Microbiology, 23rd edition. McGraw Hill Publishers. USA.

Champoux J.J, Neidhardt F.C, Drew W.L and Plorde J.J (2004). Sherris Medical Microbiology: An Introduction to Infectious Diseases. 4th edition. McGraw Hill Companies Inc, USA.

Dictionary of Microbiology and Molecular Biology, 3rd Edition. Paul Singleton and Diana Sainsbury. 2006, John Wiley & Sons Ltd. Canada.

Engleberg N.C, DiRita V and Dermody T.S (2007). Schaechter’s Mechanisms of Microbial Disease. 4th ed. Lippincott Williams & Wilkins, Philadelphia, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA. Pp. 902-903.

Murray P.R, Baron E.J, Jorgensen J.H., Pfaller M.A and Yolken R.H (2003). Manual of Clinical Microbiology. 8th edition. Volume 1. American Society of Microbiology (ASM) Press, Washington, D.C, U.S.A.

Murray P.R, Baron E.J, Jorgensen J.H., Pfaller M.A and Yolken R.H (2003). Manual of Clinical Microbiology. 8th edition. Volume 2. American Society of Microbiology (ASM) Press, Washington, D.C, U.S.A.

Prescott L.M., Harley J.P and Klein D.A (2005). Microbiology. 6th ed. McGraw Hill Publishers, USA.



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