Normal Flora and Their Various Location in the Body

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Normal Flora MLTGEEKS

The internal tissues of a healthy human being, e.g. brain,blood, muscle, etc., are normally sterile or  free of microorganisms.But the surface tissues of the human body that is the skin and mucous membranes are frequently in contact with environmental organisms and become readily colonized by these various environmental microbial species.

The mixture of those organisms regularly found at any anatomical site of the human body is called normal flora,natural flora,healthy flora,good bacteria or bacterial flora. Human normal flora consists of some eukaryotic fungi and protists, but bacteria are the most numerous and obvious microbial components of normal flora(human microbiome)

A healthy fetus in the uterus is free of microorganisms. During birth, the infant get exposed to vaginal flora. Within a few hours after birth,oral flora and nasopharyngeal flora develops and on a day or two,resident flora of the small intestine(intestinal flora or intestinal microflora) also appears.


The term ” normal microbial flora ” refers to the population of microbes living in the skin (skin microbes) and mucous membranes of healthy normal people. The microorganisms on skin and mucous membranes are arranged in two groups:

A. The resident flora

These consists of relatively fixed types of microorganisms found in a given area and at a given age; if disturbed, it recovers quickly.

   B. The transient flora

These consists of non – pathogenic or potentially pathogenic microorganisms that mostly inhabit the skin or mucous membranes for hours, days or weeks;They are derived from the environment,does not cause disease and it doesn’t  permanently established itself on the skin or surface or mucous membranes.These transient flora members are generally of little significance as long as the normal resident flora remains intact.However, if the resident flora is disturbed, transient microorganisms can colonize, grow and produce diseases.


It consists of organisms that are regularly present in a particular area of the body and when disturbed, it re – establishes itself and a good example of such microorganism is  Escherichia coli which is resident normal flora of the intestine and is one of the types of intestinal bacteria.

The role of the resident flora

Those microorganisms which are constantly present on the surface of the body are known as commensals microorganism.The growth of these commensals microorganism in a given area depends upon some physiologic factors such as  moisture,temperature and the presence of certain nutrients including inhibitory substances.

The resident flora of certain body regions plays a crucial role in maintaining health and normal function.Members of the resident flora in the intestinal tract synthesize vitamin K and help absorb nutrients.On the skin and mucous membranes, the resident flora may prevent colonization by pathogens and possible disease through “ bacterial interference. ” The mechanism of bacterial interference is not clear.It may include competition for nutrients,competition for receptors or binding sites on host cells, mutual inhibition by metabolic or toxic products, mutual inhibition by antibiotic materials or bacteriocins, or others mechanism.

Also read  Dermatophyte Test Medium principle and colonies morphology

The suppression of normal flora tends to be filled with organisms from the environment or from other parts of the body, and such organisms act as opportunists and can become pathogens.

On the other hand, under certain circumstances, members of the normal flora can themselves cause disease, and if they are removed from the confines of that environment and introduced into the bloodstream or tissues, these organisms can become pathogenic taking an example of  streptococci viridans  which is one of the most common resident organisms of the upper respiratory tract and if in case, large numbers of these microorganism are introduced into the bloodstream (eg, following tooth extraction or tonsillectomy), they may settle on deformed or prosthetic heart valves and produce infective endocarditis.

Small numbers transiently occur with minor trauma like dental scaling or vigorous brushing.Bacteroid species are the most common resident bacteria that cause suppuration and bacteremia when introduced into the free peritoneal cavity or pelvic tissues along with other bacteria as a result of trauma.

There are many other examples, but the important point is that microbes of normal resident flora are harmless and can be beneficial at their normal location in the host and in the absence of concurring abnormalities.They can cause diseases if they are introduced in large numbers into foreign locations and if predisposing factors are present.

Advantages of Resident Normal Flora

  • They prevent or suppress pathogen entry.
  • They synthesize vitamins in particular Vitamin K and various B group vitamins.
  • The normal flora evokes the production of Antibodies. These antibodies interact with pathogens that have related or shared antigens, thereby increasing the host’s immune status against the invading pathogen.
  • Colonies produced by some normal flora organisms have a harmful effect on the pathogens.
  • Endotoxins released by normal flora can help the body’s defense mechanism

Disadvantages of Resident Normal Flora

  • When the immune system is weak or compromised, they become pathogenic.
  • They may act as pathogens in different situations (other than their normal habitat) e.g. normal intestinal flora may cause urinary tract infection (UTI).
  • Normal flora can cause diagnosis confusion due to its ubiquitous presence in the body and its resemblance to some pathogens.

List of some resident normal flora and their sites in the body

Sites Resident normal flora genera
Upper respiratory tractFusobacterium
MoraxellaCandida (Fungus)
Upper Digestive TractActinomyces
Lower Digestive TractBacteroides
Also read  Introduction to Medical Mycology and importance of Fungi


They consists of both non – pathogenic and potentially pathogenic bacteria which inhabit the body surface or mucous membranes for a limited period of time.They can be removed from the body surface by mechanical means such as meningococcus and Pneumococcus can be removed from the human nasopharynx from time to time.These members of the normal flora form part of the host and they include saprophytes, commensals, facultative pathogens and true pathogens.

Normal skin flora

The skin is constantly exposed to and in contact with the environment and is particularly susceptible to transient microorganisms.The predominant resident skin microorganisms are the aerobic and anaerobic diphtheroid bacilli  like Corynebacterium and Propionibacterium; those non-hemolytic aerobic and anaerobic staphylococcus species such as Staphylococcus epidermidis, occasionally Staphylococcus aureus and Peptostreptococcus species; gram – positive, aerobic, spore – forming bacilli that are ubiquitous in air, water and soil such as the alpha hemolytic streptococci (viridans streptococci) and enterococci (enterococcus species);and gram – negative bacilli coliform and acinetobacter

A low pH value, fatty acids in the sebaceous gland secretions and the presence of lysozymes are important factors to remove non – resident microorganisms from the skin. Normal skin inhabits 102-104 organisms / square.Cm.The following are normal flora of the skin surface

Skin Staphylococcus epidermidis
Streptococcus viridans
Escherichia coliCandida

Normal flora of the conjunctiva

The conjunctiva is relatively free of bacteria as lysozyme is present in the tears that flush the bacteria. The following are predominant eye normal flora organisms

Eye (Conjunctiva)Moraxella species
Staphylococcus epidermidis
Moraxella species
Non hemolytic streptococci

Normal Flora from the mouth

The mouth contains micrococcus, gram – positive aerobic spores containing bacilli, coliforms, proteus and lactobacilli.The gum pockets between the teeth and crypts of the tonsils have a broad spectrum of anaerobic flora such as spindle-shaped bacilli, treponemas, lactobacilli Candida etc

The mouth of a child is not sterile at birth.It generally contains the same types of microorganisms as found in the mother ’s vagina.These bacteria decrease in number and are replaced by similar bacteria that are present in the mouth of mother and carer.

Normal flora of the nose and nasopharynx

The child’s nasopharynx is sterile at birth, but in 2 – 3 days it acquires the flora carried by the mother and the companions. Nasopharynx is a natural habitat of the most common pathogenic bacteria that cause infections of the throat,nose, lungs and bronchi.

Also read  Widal Slide and tube test principle and result interpretation

The nose harbors the following flora.

Moraxella lacunata

Upper Respiratory Normal Flora

Within 12 hours after birth, alpha-hemolytic streptococci are found in the upper respiratory tract and become the dominant organism of the oropharynx and remain so for life. A similar flora is established in the pharynx and trachea. Smaller bronchi and alveoli are usually sterile.

Normal flora of the urogenital tract

Mycobacterium smegmatis, a harmless commensal, can be found in the secretions (smegma) of the male and female genitals.They can cause  confusion with the tubercle bacilli.Mycoplasma and ureaplasma strains often occur as part of the normal flora.

Gardnerella vaginalis, bacteroids and alpha streptococci have been found or isolated  in the urethra penile.As for the female urethra,it is either sterile or contains staphylococcus epidermidis.

The vagina of a newborn baby is sterile but  within 24 hours it is colonized by micrococci and enterococci.In 2 – 3 days time,there is also an appearance of doderlein’s bacillus and  this causes a change in flora depending on the pH value of the vagina.These doderlein bacilli remain in the vagina until menopause.

Normal flora of the gastrointestinal tract

The gastrointestinal tract of the fetus in utero is sterile. It is contaminated with organisms shortly after birth. In breastfed infants, the intestine contains enterococci,lactobacillus, colon bacilli and staphylococci.

In infants fed by bottle, the intestine contains anaerobic lactobacilli(good bacteria in stomach), colon bacilli and aerobic and anaerobic spore-bearing organisms. With the change of food the flora changes. The diet has a clear influence on the composition of the intestinal and stool flora.

If the pH value in the stomach is low, the stomach is sterile, but if the pH value in the small intestine increases, the number of bacteria progressively increases via the duodenum to the large intestine.The bacterial count in the small intestine is low in comparison to the large intestine.enterococci and Lactobacilli  dominate in the duodenum and in the proximal ileum.Bacterial flora is similar in the lower ileum, caecum and rectum.The anaerobic state of the colon is maintained by aerobic bacteria that use free oxygen.

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About the Author: Arthur Westmann

DEFFE ARTHUR (AMOEBAMANN) is the founder and author of MLTGEEKS and MLTEXPO.He’s from Cameroon and is currently a Final year State Medical Laboratory Technician (MLT MA). Beyond lab works, he’s a passionate internet user with a keen interest in web design and blogging. Furthermore He likes traveling, hanging around with friends and social networking to do in his spare time.

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