Normal Microbiota of the Healthy Human body

Normal microbiota of human body


  • Microorganisms have significant roles in human survival, an adult human body is consisting of a lot more than millions of microorganisms inhabiting the human body.
  • These microorganisms mostly bacteria comprise the normal microbiota.
  • They inhabit mainly the exterior surface of the skin, and inner surfaces of the oral cavity, upper respiratory, intestinal tract, and genitourinary tract.
  • Microorganisms adapted to live & multiply in the harsh environment of the host body for e.g., acidic pH in the stomach.
  • Most microflora are safe, they don’t cause diseases
  • They are even beneficial to the host and live as commensals.
  • Some normal microbiota is opportunistic pathogens, they might cause disease in favorable conditions like wound injury or immunity of body decreases.
  • Some factors affect microflora such as age, hormonal state, health, personal hygiene, antibiotics intake.
  • The microbiota falls into two types of state, based on the duration of stay:
    • Resident– are fixed type of microorganisms, establish their niche at one body site at a particular age according to their genetic, morphological, and physiological properties. They re-establish if eliminated from the site.
    • Transient– are temporary microorganisms acquire from the diversity of microorganisms present in the environment, might be pathogenic or non-pathogenic, and could be excluded by resident microorganisms or host defense system.
  • In case of pathogenic involvement without any adverse consequences on the host, the state is called carrier state.
  • Significance of normal microbiota – Commensal populations participate in the metabolism of food, provides protection against pathogenic microorganisms, and triggers the host immunity.

Body Sites devoid of Microorganisms

  • Blood.
  • Lower respiratory Tract.
  • Cerebrospinal fluid (CSF).
  • Urinary Bladder, Tissues.

Origin of Microbiota

  • Before birth, the fetus is sterile, i.e., free of bacteria.
  • Under natural circumstances, the fetus acquires microorganisms from the birth canal by surface contact.
  • Initially, microflora colonizes at particular sites in absence of competitors.
  • Each area of the human body, with its special environmental conditions, has its own particular mixture of microorganisms. For e.g., the oral cavity acquires different microbial populations than the intestines.

Factors affecting the normal microbiota

  • Types of available nutrients, pH of the site, oxidation-reduction potential
  • Resistance to antibacterial substances present in host site which include bile and lysozyme.
  • Colonization factor- Adhesin- mediated affinity for epithelial cell receptors.
  • Microbial interaction includes microflora competing for the nutrients and adaptation to inhibit the thriving of others microorganisms by antibiotics & bacteriocins production.

Normal Microbiota at the different sites

  • The total microbiota of the human body constitutes more than 1000, diverse species of microorganisms. It may prevent or cause disease.
  • Bacteria are predominant, but fungi mainly yeasts, protozoa, and viruses can exist in normal microbiota, their numbers are less as compared to bacteria.
  • The virus usually doesn’t identify as a true normal flora, even though some exist in cells without causing symptoms, for e.g., certain human intestinal viruses were discovered in tissue culture with cytopathogenic effect, they were termed as “orphan virus”, one more is coxsackie viruses obtain from human hosts which affect mice.

 Blood, Body fluid & Tissues

  • In a healthy host, they are sterile but occasionally organisms may penetrate through epithelial cells during childbirth or trauma, cause bacteremia (blood infection) can damage heart valves.


  • The skin constitutes the epidermis, exterior surface, and dermis, connected with the tissue layer.
  • The epidermis is dead. anucleated cells, constantly in contact with microorganisms from the environment, its impermeable to bacteria however cuts, abrasion, or burns can allow bacteria to penetrate.
  •  The skin surface is not favorable for the most kind of bacteria for their growth and multiplication. For e.g., Streptococcus pyogenes doesn’t survive more than few hours because of several factors discouraging skin colonization.
    • Dryness– inhibits microbial growth.
    • Low pH- 3-5, due to lactic or other organic acid production by Staphylococcus epidermis, discourage other microbial growth
    • Inhibitory substances, such as lysozyme produce by sweat glands which disrupt bacterial cell walls, sebaceous glands secrete complex lipids, which partially degrade by few bacteria like Propionibacterium acnes.
  • Sweat glands also produce peptides having an antimicrobial property called cathelicidins, it form pores in bacterial plasma.
  • Common microorganisms found on the skin are Staphylococcus aureus, Propionibacterium, Corynebacterium, Staphylococcus epidermis.
  • Pityrosporum ovale & orbiculare commonly occur on the scalp.
Schematic representation of the Skin Structure


  • The continuous secretion of saliva through the mouth exerts mechanical flushing action that removes many microorganisms.
  • The epithelial cell’s desquamation is the second mechanical factor that removes microorganisms present in the oral cavity.
  • Saliva is composed of amino acids, lipids, carbohydrates, water, and inorganic compounds, serves as nutrition for bacteria, generally, saliva has 108 bacteria/ml.
  • The mouth consists of most alpha-hemolytic streptococcus such as Streptococcus oralis, S. milleri, S. salivarius, abundant numbers of diphetheroids are also mainly present.
  • Near the tonsils, Micrococcus are abundant, there is a number of anaerobes mainly present, such as Porphyromonas, Fusobacterium, and Prevotella.
  • Streptococcus mutans cause tooth decay, by adhering to the tooth surface, glucan is formed only in presence of sucrose, enzymatic reaction produces fructose which is fermented by Streptococci releasing lactic acid which etches the surface of the tooth. Other invaders such as Lactobacillus and Actinomyces and organic matter aggregates on the surface of teeth which is called plaque, consisting of a high number of bacteria around 108 cells/mg.


  • There are a few bacteria that live in commensal mainly found in the conjunctiva of the eye. The abundant bacteria is Staphylococcus epidermis followed by SaureusHaemophilus spp., and Streptococcus pneumonia.


  • The normal microbiota of the external ear is similar to skin, Staphylococcus, Corynebacterium, some fungal strains such as Aspergillus, Alternaria, PenicilliumCandida, and Saccharomyces.

Respiratory Tract

  • The respiratory tract lined with mucous membranes is not favorable for colonization of bacteria because cilia exist on nasopharynx epithelial cells that propel the microorganism down the oropharynx, where bacteria is swallowed and destroyed by acid.
  • Nasal mucus has a bactericidal effect exerted by lysozyme.
  • Despite these factors, the nose as well as the nasopharynx inhabit numerous normal microflora, adapt to adhere to the epithelial cell layer of mucous membranes.
  • The predominant bacteria present in the nose are Staphylococcus epidermisS. aureus; in the nasopharynx, avirulent  Streptococcus pneumonia and other α- hemolytic streptococci are abundant, other microorganisms such as Corynebacterium, Neisseria, Branhamella, Haemophilus, and Micrococcus are commonly found.
  • The mucous membranes of the trachea (windpipe) and the branches (bronchii) lack normal microbiota, because of the upward cilia-driven flow of mucus and alveolar macrophages, phagocytic cells are present which engulf and destroy bacteria.


  • The stomach constantly receives numerous microorganisms from the oral cavity, fluid contents of the healthy stomach, have <10 bacteria/ml, because of bactericidal effect of the hydrochloric acid secretion in the stomach.
  • Few microorganisms are mainly found such as Candida spp., Peptostreptococcus, Streptococcus, Staphylococcus, Lactobacillus, which may survive when they rapidly leave the stomach, or organisms ingested with food may be resistant to gastric pH e.g., Mycobacteria.

Small Intestine

  • The upper portion, the duodenum has few bacteria mainly gram-positive cocci around less than 103 because of the combined influence of the stomach’s acidic juices, and inhibitory action of bile and pancreatic secretions
  • In the jejunum, mainly species of enterococci, lactobacilli, and diphtheroid, as well as Candida spp may be also present.
  • In the ileum, microflora resembles to the large intestine mostly anaerobic bacteria as well as members of the family Enterobacteriaceae are present.

Large Intestine

  • The large intestines [colon] have the largest microbial community in the human body.
  • Over 400 various species have been found from human feces.
Large Intestine Microbiota
A smear of feces, showing the diversity of microorganisms
  • It primarily consists of, gram-negative and gram-positive, anaerobic bacteria,  spore-forming and non-sporing rods.
  • Many bacteria like Candida albicans present in the large intestine occur as commensal.
  • The anaerobic gram-negative bacilli include species of Bacteroides (B. gragilis , B. oralis), and fusobacterium.
  • The gram-positive bacilli include Bifidobacterium, Eubacterium, and lactobacillus.
  • The facultative anaerobic species found in intestines of  the genera Escherichia, Proteus, Klebsiella, and Enterobacter
  • Trichomonas hominins, Entamoeba hartmanni, Iodamoeba butschlii, and Endolimax nana are mainly found.

Genitourinary Tract

  • The upper genitourinary tract includes kidneys, ureters, and urinary bladder are free from microorganisms.
  • In both males and females some bacteria is usually present in the distal portion of the urethra for e.g., Staphylococcus epidermis, Enterococcus faecalis & corynebacterium,
  • In adult females, because of large surface and mucosal secretions has a distinct microbiota constantly changing with the menstrual cycle.
  • The predominant microorganisms are acid-tolerant lactobacilli mainly Lactobacillus acidophilus, they ferment glucogen produce in vaginal epithelium and produce lactic acid, which results in, acidic pH of the vagina and cervix around 4.4- 4.6, inhibiting other microorganisms.
Lactobacillus, predominantly found in vaginal epithelial cell

Role of Microbiota in Disease

  • Many species act as opportunists which are present in normal microbiota, which can cause infection when they are high in number or the host defense system is compromised.
  • For e.g., Strains of E.coli infect the urinary bladder through the urethra, which leads to acute urinary tract infection, generally in a sexually active woman.
  • Viridians Streptococci, present in the oral cavity, may breach into the blood in case of injury [ like tooth extraction] or maybe trauma and colonize heart valve which is previously damaged, which causes bacterial endocarditis.
  • The compromised immunity weakens the immune response, which leads to defects in phagocytic activity or the weakening of innate barriers by vitamin deficiency.
  • Most infections are accounted for in immunocompromised patients e.g., diabetes, cancer, AIDS.

Beneficial effects of the Microbiota

  1. Develop Immune Response
    • Microbiota helps in developing immunologic competence.
    • Experimentally, it was concluded, animals raised in aseptic conditions have underdeveloped reticuloendothelial systems, low antibodies count in serum.
    • More the exposure to diverse microflora, the more immunity of the host is developed.
  2. Exclusionary Effect
    • The microbiota produces such conditions which restrict the colonization of pathogens.
    • In breastfeeding infants, bifidobacteria present in the colon produce an environment that is unfavorable for colonization of enteric bacteria; a similar protective effect is provided by maternal IgA, from mother milk.
    • Antibiotic therapy, especially with a board- spectrum agents, may change the normal microflora present in the gastrointestinal tract; it may be replaced by antibiotic-resistant organisms.
    • Experimentally, it has been concluded, exclusionary effects of the microflora provide competition against the pathogen colonization in the cells of the host.
    • For e.g., In the germ-free rat,  albicans attaches to oral epithelial cells, however prior colonization of viridans streptococci prevent the establishment of C. albicans
  3. Production of Essential Nutrients
    • In ruminants like cows, the action of anaerobic microbiota in the rumen is essential to the nutrition of the animal.
    • The normal microbiota digests cellulose and provides vitamin B required by the host.
    • In the human hosts, microbiota produces vitamin B and K, antibiotic therapy reduced the ability of the microbiota to produce vitamins.

Reference and Sources


Also Read:

Leave a Comment

Exit mobile version