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Microbiota which can also be called normal microflora is the totality of microorganisms that are inherently present in a particular environment, body or location at every specific point of time. Mycoflora are fungal organisms that live in particular sites of the body as normal flora without causing infection or disease. Microbiota goes into competition with pathogens found on- and in- the human body with a view to subverting their pathogenic and virulent activities within the host. They do this through a process called amensalism (a bacterial interference mechanism). In amensalism, normal microflora utilizes available space, nutrients, water and other resources (required by the pathogen to cause infection and disease) in the host and produce substances that resist their disease-causing mechanisms in the host. Amensalism is an adverse microbe-microbe interaction in which the product or activity of one microorganism has a harmful effect on another microorganism.


However, microbiota can turn form being harmless microorganisms to becoming potential pathogens to a host in some exceptional cases. Others can also become opportunistic microorganisms which only cause disease in the host by chance i.e., when the environment or body of the individual favors their blossoming (e.g., in an immunocompromised case such as in an HIV/AIDS patients or an individual whose immune system has been suppressed due to chemotherapy). The overuse of antibiotics, stress and nutritional imbalance in human beings can cause their microbiota to become pathogenic in nature. It should also be noted that different materials and substances (whether clinical or of non-clinical origin) have their own microflora which are well-known and very unique to them.

The microbiologist should acquaint him or herself on the basic knowledge of the different microbiota that make up different parts of the human body or the environment from which the samples they will be working with in the laboratory are actually made up of. This will allow the scientist to make concrete conclusions on the inferences drawn from a particular research or test so that the final judgment of an experiment is not based on the microbiota (which are not harmful and might not necessarily be the target or cause of the malady being deciphered). The human body is well inundated with beneficial microorganisms which help to keep infectious organisms at bay; and these organisms (i.e., normal microflora) confer other health benefits to the individual (Figure 1). It is worth mentioning that the foetus in the womb of a pregnant woman (i.e., in utero) is free from normal microflora. Humans starts developing and forming their microbiota few seconds after delivery as microorganisms colonizes their external and internal body parts. Infants become colonized with a plethora of microorganisms and commensals which all constitutes their normal microflora; and this process of microbiota colonization in the infant commences soon after birth and this continues as the infant grows. Some internal tissues of a healthy human being including blood, brain cells, muscles and cerebrospinal fluid (CSF) are normally germ-free i.e., they are free from microorganisms including normal flora, and are said to be sterile. However, in the presence of an infection or disease, these seemingly sterile fluids of the human body (e.g., CSF) will become contaminated by pathogenic microorganisms, and samples taken for culture in the laboratory usually comes out positive because of the presence of pathogens in them.

Figure 1: Human anatomy showing sites of the body colonized by microorganisms. Photo courtesy:

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 unutilized 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, and introduction of other types of food apart from breast milk. 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. A summary of some of the microbiota or normal microflora of the human body and their location is shown in 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) and other beneficial molecules 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 HIV/AIDS (Table 1). The irrational use of antibiotics without prescription clears the normal flora in the body, and this allows pathogens to thrive and proliferate, thereby causing infection or disease in the individual.  

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 disease 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. However, the normal flora in the host’s body also helps to checkmate the establishment of infection or the development of disease in conjunction with the immune system. The inappropriate use of antibiotics can destabilize the normal flora in the body and allow pathogens to establish themselves, thereby causing infection or disease in the host.

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

Pseudomonas, Enterobacteriaceae, coagulase-negative Staphylococci (CNS), Diphtheroids    Outer ear  Otitis media, sepsis, bacteraemia and 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 and streptococcal infections, septicaemia, bacteraemia  
Streptococci, CNS, Haemophilus, Staphylococci  Eye (conjunctiva)Conjunctivitis, bacteraemia, pneumonia 
Enterobacteriaceae, Lactobacilli, Clostridium, Enterococci, Mycobacterium, Bacteroides  Small intestine  Bacteraemia and 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 and bacteraemia  
Fusobacterium, CNS, Peptostreptococci, Streptococci, Bacteroides, Mycobacterium  Urethra  Urethritis and sepsis
Helicobacter, Streptococci, Enterobacteriaceae, Staphylococci, Lactobacillus, Peptostreptococci  Stomach  Septicaemia and bacteraemia
  Neisseria, CNS, Haemophilus, Staphylococci, streptococci  Nose  Upper respiratory tract infection
Clostridium, Candida, Lactobacilli, Gardnerella, Diphtheroids, Bacteroides, Streptococci, Peptostreptococci   Vagina  Vaginitis, candidiasis and urethritis  


  1. They make a healthy human being to be less susceptible to pathogens.
  2. They help in stimulating the immune system against pathogens.
  3. They prevent the invasion and colonization of pathogens in and on the body.
  4. They provide protection against infections on the sites of the body (internal or external) they are located.
  5. They prevent pathogens from colonizing certain parts of the human body. For example, Lactobacillus acidophilus, a resident microflora of the vagina of women produces lactic acid from the fermentation of glycogen. This maintains a weakly acidic environment that prevents pathogens like Candida albicans and other aerobic bacteria from colonizing the adult female vagina.They also prevent the adhesion of pathogens on the human skin and other parts of the body including the mucosal surfaces.
  6. Intestinal microbial flora produces vitamin B12 and vitamin K (which are not manufactured by humans) in the gut.
  7. Intestinal microbial flora helps in the production of organic acids and gases (known as flatus) in the gut of humans and animals.
  8. They inhibit the growth of pathogens in the body by producing chemical substances that antagonizes the activities of the invading pathogenic microbe.
  9. Normal microflora produces important vitamins in the body such as cobalamin (vitamin B12) in the gut. They are also believed to stimulate the immune system by producing certain natural antibodies that fights invading antigens.
  10. Knowledge on the microbiota found in and on different parts of the body helps a microbiologist to be acquainted with the likely infection/disease that will develop in a particular body site and, the type of microorganism to anticipate from the culture of specimens from such body locations.

Further reading

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

Gilligan P.H, Shapiro D.S and Miller M.B (2014). Cases in Medical Microbiology and Infectious Diseases. Third edition. American Society of Microbiology Press, 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.

Mahon C. R, Lehman D.C and Manuselis G (2011). Textbook of Diagnostic Microbiology. Fourth edition. Saunders Publishers, USA.

Patrick R. Murray, Ellen Jo Baron, James H. Jorgensen, Marie Louise Landry, Michael A. Pfaller (2007). Manual of Clinical Microbiology, 9th ed.: American Society for Microbiology.

Wilson B. A, Salyers A.A, Whitt D.D and Winkler M.E (2011). Bacterial Pathogenesis: A molecular Approach. Third edition. American Society of Microbiology Press, USA.

Woods GL and Washington JA (1995). The Clinician and the Microbiology Laboratory. Mandell GL, Bennett JE, Dolin R (eds): Principles and Practice of Infectious Diseases. 4th ed. Churchill Livingstone, New York.

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