Normal Flora of the Human body

18 December 2021

Normal Flora of the human body is the various bacteria and fungi that are permanent residents of certain body sites. Microorganisms that live on another living organism (human or animal) or inanimate objects without causing any harm are called normal flora. The term Human Microbiome is often used to describe the normal flora of the human body. Viruses, and parasites (protozoa and helminths), which are the major groups of microorganisms, are usually not considered members of normal flora, although they can be present in asymptomatic individuals. The human body has ten times more microbes than normal body cells. The largest and most complex microbial population lives in the colon. Normal flora is acquired shortly after birth and changes continuously throughout life. 


They are present on parts of the body that are exposed to or communicate with the external environment such as the skin, nose, mouth, and gastrointestinal and urogenital tract. Numbers and types of microorganisms vary at different sites of the body. The internal organs are usually sterile except for the occasional transient organism.

Normal flora relationship to host may be symbiotic or commensalism. Commensals are organisms that derive benefits from the host but do not cause any harm. Most human microbes are commensals.  Symbiosis relationships exist when both host and microorganism live together with mutual benefits, such as gut flora. The gut provides a warm moist environment and flora gives a natural barrier against many invading pathogens.


carrier means that a person harbors a potential pathogen and therefore can be a source of infection to others. The term is frequently used in reference to a person with an asymptomatic infection or to someone who has recovered from disease but continues to carry the organism and may shed it for long period. The term colonization refers to the acquisition of new organisms. 

Members of normal flora play a role both in the maintenance of health and in the causation of disease in the following ways:

  • Although these organisms are nonpathogens in their usual sites, they can cause diseases at other locations, especially in immunocompromised and debilitated individuals.
  • They prevent the colonization of pathogens by competing for attachment sites. This is the most important function of gut flora.
  • Intestinal bacteria synthesize several B- vitamins and vitamin K.
  • They Stimulate the production of antibodies that cross-react with similar antigens and pathogens. Gut flora influences the maturation and function of the immune response. There is evidence that microbes play an important role in several body functions and diseases such as weight control, inflammatory bowel disease, the immune response in general, and resistance to infectious diseases.

Some studies implicate dysbiosis or imbalance of gut flora in the development of various autoimmune diseases such as Lupus, Inflammatory bowel diseases, Multiple Sclerosis, Rheumatoid Arthritis, Type-1 Diabetes, and even colon cancer.

Normal Flora of Skin

The predominant organism is staphylococcus epidermidis which is non-pathogenic on the skin but can cause infection in other places such as artificial heart valves or prosthetic joints. There are about 1000-10,000 organisms per cm2 of skin. Most are on the upper layer of skin and some are found in hair follicles. 

Other less important organisms on the skin are staphylococcus aureus, Corynebacterium (diphtheroids), various streptococci, Pseudomonas aeruginosa, Candida albicans, and anaerobes. Anaerobic microorganisms such as propionic bacterium and Peptococcus are found deep in hair follicles. Propionibacterium acnes is a common bacterium that is implicated in the pathogenesis of acne.


Normal Flora of Respiratory Tract

A wide variety of microorganisms are found in the nose, throat, and mouth, but the lower bronchi and alveoli contain a few if any organisms. The nose is colonized by various streptococci and staphylococci and diphtheroids. Staphylococcus aureus is important in nose.

The throat contains, Streptococci viridans, Neisseria species, and Staphylococcus epidermidis. These occupy attachment sites and inhibit the growth of pathogens such as streptococcus pyogenes, Neisseria meningitis, Staphylococcus aureus, and Haemophilus influenza. The main members of the normal flora of the mouth and throat are the Viridans streptococci, such as Streptococcus sanguinis and Streptococcus mutans.


Viridans streptococci are the most common cause of subacute bacterial endocarditis. Streptococci viridans make up about half of the bacteria. Streptococcus mutants are found in large numbers in dental plaque. The entrapped bacteria in gelatinous materials produce a large amount of acid which demineralizes the enamel and initiates carries. Anaerobic bacteria like Bacteroides, Prevotella, Fusobacterium, Clostridium, and Peptstreptoococcus, Actinomyces israelii are found in gingival crevices. Eikenella corrodens is also found in the normal flora of the mouth. 

Normal Flora of Intestinal Tract

The stomach contains very few organisms because of low PH. The proximal small intestine has a relatively sparse gram-positive flora, consisting mainly of lactobacilli and Enterococcus faecalis and yeast, particularly Candida albicans. The distal part of the small intestine contains greater numbers of bacteria and additional species, including coliforms (Escherichia coli and relatives) and Bacteroides, in addition to lactobacilli and enterococci.


The colon is the major location of bacteria in our body. 90% are anaerobes. The most abundant facultative anaerobe bacteria are coliforms of which Escherichia coli is the most important. There are both gram-positive and gram-negative rods and cocci. (Bifidobacterium, Eubacterium, Fusobacterium, Lactobacillus, Enterococcus faecalis, various aerobic gram-negative rods and other streptococci, Clostridium, Pseudomonas aeruginosa). The normal flora of the intestinal tract can cause diseases at other sites, for example, E. coli causes urinary tract infection and B. fragilis cause peritonitis associated with perforation of the intestinal tract following trauma, appendicitis, diverticulitis. Other important anaerobic pathogens include Fusobacterium and Peptostreptococcus and facultative bacteria include Enterococcus faecalis which cause UTI and endocarditis.

Broad-spectrum antibiotics therapy for prolonged duration can suppress the normal flora, allowing rare antibiotic-resistant toxin-producing bacteria Clostridium difficile to overgrow causing pseudomembranous colitis.


Normal Flora of Urogenital Tract

Urine in the bladder is sterile in a healthy person, but during the passage, through the outermost part of the urethra, it becomes contaminated with S. epidermidis, coliforms, diphtheroid, and non-hemolytic streptococci.

The vaginal flora of adult women consists primarily of lactobacillus species. They produce acid and keep PH low and prevent the growth of potential pathogens. Lactobacillus are less in number before puberty and after menopause so vaginal PH increases. Fecal flora especially E. coli and Enterobacter can cause recurrent UTIs. 15-20 % of women have group B streptococci in the vagina which causes sepsis and meningitis in newborns acquired during delivery. 5 % have staphylococci which can cause toxic shock syndrome. Staphylococcus saprophyticus can also cause urinary tract infections in women. Other organisms in the vagina include various streptococci, diphtheroids various gram-negative rods, Bacillus.


Normal Flora and their anatomical locations:

Members of the Normal FloraAnatomical Locations
Bacteroides speciesColon, Throat, Vagina
Candida albicansColon, Mouth, Vagina
Clostridium speciesColon
Corynebacterium species
Nasopharynx, Skin, Vagina
Enterococcus faecalisColon
Escherichia and other ColiformsColon, Vagina, outer urethra
Gardnerella vaginalisVagina
Haemophilus speciesNasopharynx
Lactobacillus speciesColon, mouth, Vagina
Neisseria speciesMouth, Nasopharynx
Propionibacterium acnesSkin
Pseudomonas aeruginosaColon, Skin
Staphylococcus aureusNose, Skin
Staphylococcus epidermidisSkin, nose, mouth, Vagina
Viridans streptococci Mouth, Nasopharynx

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