Normal microbial flora and their Roles in the Human Body

  • The term “normal microbial flora” denotes the population of microorganisms that inhabit various body parts like skin and mucous membranes of healthy normal persons.
  • Our skin and mucous membranes always harbor a variety of microorganisms that can be categorized into two groups:
    • The resident flora:
      • It consists of relatively fixed types of microorganisms regularly found in a given area at a given age.
      • If disturbed, it promptly reestablishes itself.
    • The transient flora:
      • It consists of non-pathogenic or potentially pathogenic microorganisms that inhabit the skin or mucous membranes for hours, days or even weeks.
      • It is derived from the environment, doesn’t produce disease, and doesn’t establish itself permanently on the surface.
  • If the resident flora is disturbed, transient microorganisms may colonize, proliferate and produce disease.

Normal flora of the skin:

  • Because of its constant exposure to and contact with environment, the skin is particularly suitable to contain transient microorganisms.
  • The predominant resident microorganisms of the skin are:
    • Aerobic and anaerobic diphtheroid bacilli (e.g. Corynebacterium, Propionibacerium). Propionibacerium acne which metabolizes sebum is found associated with sebaceous glands.
    • Non-hemolytic aerobic and anaerobic staphylococci (e.g. Statphylococcus epidermidis), other coagulase-negative staphylococci, occasionally aureus, and Peptostreptococcus species)
    • Gram-positive, aerobic, spore-forming bacilli
    • Alpha-hemolytic streptococci (viridans streptococci) and enterococci (Enterococcus species),
    • Gram-negative coliform bacilli and Acinetobacter
    • Acid-fast, non-pathogenic mycobacteria ( smigmatis) occur in areas rich in sebaceous secretions (genitalia, external ear)
    • Fungi and yeasts are often present in skin folds
  • Skin consists of outer epidermis and inner dermis layer with hair follicles, sweat glands and sebaceous glands.
  • Although skin contains large number of organisms, many factors of skin discourage the colonization of non-resident bacteria in skin. Some such factors are:
    • Dryness of the skin: Dry skin is inhibitory to the microorganisms. Skin is somewhat moistened by the secretion of sweat and sebaceous glands. Skin of webs, toes, nipple and genital areas are rich in these glands. So these relatively moist and humid areas are rich in normal flora than other skin parts.
    • Acidic/ Low pH: Skin has normal pH between 3 and 5, which discourages the growth of most microorganisms.
    • Inhibitory/ Antimicrobial substances: Skin contains many antimicrobial substances such as lysozyme which is secreted by sweat glands and lactic acid and lipids (fatty substances) which are secreted by sebaceous glands.
    • Vigorous daily scrubbing with soap containing hexachlorophene and other disinfectants can diminish the transient flora on the skin.
  • Despite the above mentioned inhibitory factors, many microorganisms which can tolerate such factors are found on the skin.

Normal flora of the mouth:

  • Abundant moisture and presence of food facilitates rapid growth microorganisms in mouth. However, flow of saliva through mouth takes many bacteria from mouth to the stomach.
  • Desquamation is another mechanism that removes microorganisms by the removal of epithelial cell layer inhabited by microorganisms.
  • The mucous membranes of the mouth and pharynx are often sterile at birth but may be contaminated by passage through the birth canal.
  • Within 4-12 hours after birth, viridans streptococci become established as the most prominent members of the resident flora and remain so for life.
  • Predominant normal flora of mouth are:
    • Early in life, aerobic and anaerobic staphylococci, Gram-negative diplococci (Neisseriae, Moraxella catarrhalis), diphtheroids, and occasional lactobacilli are added.
    • When teeth begin to erupt, the anaerobic spirochetes Prevotella species (P. melaninogenica), Fusobacterium species, Rothia species, and Capnocytophaga species establish themselves, along with some anaerobic vibrios and lactobacilli. Streptococcus mutans is found in teeth which cause dental caries.
    • Actinomyces species are normally present in tonsillar tissue and on the gingivae in adults
    • Various protozoa and yeasts (Candida albicans) also occur in the mouth.

Normal flora of the Upper Respiratory Tract (URT) and Lower Respiratory Tract (LRT)

  • Upper respiratory tract includes nasopharynx, oropharynx and throat.
  • Although many microorganisms enter the URT through air, most of them are removed by the mucous lining of the respiratory tract.
  • Microorganisms are first trapped in the mucous, then beating of cilia and movement of mucous down into the oropharynx causes the swallowing of these microorganisms and destroyed in the acidity of the stomach.
  • Furthermore, mucous also consists of lysozyme that kills many microorganisms of the mucous.
  • Some microorganisms that are able to attach to the mucous membrane form the resident flora of the URT.
    • The flora of the nose consists of prominent corynebacteria, staphylococci (epidermidis and S. aureus), and streoptococci.
    • The predominant organisms in the pharynx, are non-hemolytic and alpha-hemolytic streptococci and neisseriae. Staphylococci, diphtheroids, hemophili, pneumococci,  mycoplasmas and prevotellae are also encountered.
  • Lower respiratory tract (LRT) includes trachea, bronchi and the lungs (alveoli).
  • LRT is free from resident microbial flora.
  • As the air enters into the LRT, its velocity decreases. So, microorganisms settle on the wall of the respiratory tract and then cilia driven upward flow of mucous removes these microorganisms from the LRT.
  • Furthermore, bacteria which are able to reach the lungs are then killed by the phagocytic cells in the lungs called alveolar macrophages.

Normal flora of the Gastro-intestinal Tract (GIT):

  • Gastro-intestinal tract (GIT) consists of esophagus, stomach, small intestine (duodenum, jejunum and ileum) and large intestine.
  • Since different regions of GIT differ in their environmental, physical and chemical properties, the amount and type of normal flora are different in these regions.

Factors affecting the number and type of microorganisms in GI tract:

  • Acidity of the stomach kills many bacteria.
  • Bile salt released by gall bladder into the duodenum inhibits many microorganisms.
  • When antibiotic is taken orally, number of microorganisms decreases.
  • Form small intestine, food passes very fast into the large intestine and is stored there, hence, small intestine contains fewer bacteria than the large intestine.
  • During diarrhea, there is rapid movement of intestinal content which changes the number of bacteria.
  • Diet also affects the number and type of microorganisms.
  1. Normal flora of the stomach:
  • Stomach receives many microorganisms from mouth along with the food.
  • However, bacterial activity of HCl in stomach kills most of them. Only few organisms can tolerate this low pH in the stomach and form the resident flora there.
  • Common normal resident flora of the stomach includes Lactobaccillus, Candida albicans, Helicobacter pylori. But Helicobacter pylori is pathogenic.
  1. Normal flora of the small intestine:
  • Small intestine consists of duodenum, jejunum and ileum.
  • At birth, the intestine is sterile, but organisms are soon introduced with food.
  • Duodenum lies adjacent to the stomach and is fairly/ slightly acidic. So duodenum contains microorganisms similar to that of stomach, i.e. mainly Lactobacilli and Enterococci.
  • From duodenum to ileum, the pH gradually increases (less acidic) and hence the number of microorganisms increases from duodenum to ileum.
  • In jejunum, Enterococci, Lactobacilli, Candida albicans are found.
  • In ileum, microorganisms begin to resemble to that of the large intestine. Therefore, most common anaerobes such as bacteroids, Bififobacterium, Clostridium and facultative anaerobes such as members of Enterobacteriaceae family e.g. coli are found in the ileum.
  1. Normal flora of the large intestine:
  • Large intestine (colon) contains the largest number of microorganisms, mainly anaerobes and facultative anaerobes.
  • Facultative anaerobes utilize oxygen in colon and make it anaerobic that facilitates the growth of anaerobes. Common microorganisms found in the large intestine are:
    • Anaerobes: Bacteroids, Bifidobacterium, Clostridium perfringens, Peptococcus and Peptostreptococcus.
    • Facultative anaerobes: coli, Streptococcus faecalis, Candida albicans
    • Protozoa: Trichomonas homini

Normal flora of the genito-urinary tract:

  • In a healthy person, kidneys, urinary bladder and ureters are free of microorganisms.
  • However, anterior urethra of both the males and females contain small number of the same types of organisms found in the skin and perineum.
  • These organisms regularly appear in normal voided urine in the numbers of 102-104/ml.
  • Urethra of female (vagina) contains epidermidis, Streptococcus faecalis, Corynebacterium, Neisseria and E. coli. Occasionally.
  • Types of normal flora found in vagina depend on the menstrual cycle.
  • At puberty, aerobic and anaerobic lactobacilli appear in large numbers and contribute to the maintenance of acidic pH through the production of acid from carbohydrates, particularly glycogen. Lactobacillus breaks down glycogen into lactic acid which maintains the pH of vagina at about 4.4-4.6.
  • In general, acid tolerant microorganisms like lactobacailli, Candida albicans, Enterococci and Diphtheroids are found in vagina. Similarly, alpha-hemolytic streptococci, anaerobic streptococci (Peptostreptococci), Prevotella species, clostridia, Gardnerella vaginalis, Ureaplasma urealyticum are the normal flora of the vagina.
  • After menopause, lactobacilli diminish and a mixed flora returns in the vagina.

Normal flora of the conjunctiva:

  • Organisms like diphtheroids, epidermidis and non-hemolytic streptococci form the conjunctival microbial flora.
  • Similarly, Neisseriae and Moraxella species are also frequently present.
  • Tear contains antibacterial substance called lysozyme that holds the check in the conjunctival flora.

Role of the resident flora:

  • The microorganisms that are constantly present on the body surface are commensals.
  • Physiologic factors of temperature, moisture, and the presence of certain nutrients and inhibitory substances regulate the flourishing of normal flora in a given area.
  • Their presence is not essential to life. Yet the resident flora of certain areas plays a definite role in maintaining health and normal function.

Beneficial role:

  • Members of the resident flora in the intestinal tract synthesize vitamin K and vitamin B and aid in the absorption of nutrients.
  • On mucous membranes and skin, the resident flora may prevent colonization by pathogens and possible disease through “bacterial interference”.
  • The mechanism of bacterial interference may involve competition for receptors or binding sites on host cells, competition for nutrients, mutual inhibition by antibiotic materials or bacteriocins, or other mechanisms.
  • Many bacteria produce mucin that form mucous blanket and prevents the attachment of pathogenic microorganisms.
  • Some normal flora produces antimicrobial chemicals that kill the pathogenic organisms. E.g. coli produces colicin in intestine that kills other closely related pathogenic bacteria.
  • Some antibodies produced in response to normal flora may cross react with pathogenic bacteria having common antigens and are killed.
  • Some members of the normal flora act as opportunistic pathogens and cause diseases when bodies’ resistant mechanism decreases
  • These organisms are adapted to the non-invasive mode of life defined by the limitations of the environment.
  • If forcefully removed from the restrictions of that environment and introduced into the bloodstream or tissues, these organisms may become pathogenic.

Harmful role:

  • For example, streptococci of the viridans group are the most common resident organisms of the upper respiratory tract (URT) and if large numbers of them are introduced into the bloodstream (e.g. following tooth extraction or tonsillectomy), they may settle on deformed or prosthetic heart valves and produce infective endocarditis.
  • Bacteroides species are the most common resident bacteria of the large intestine and are quite harmless in the location. If introduced into the free peritoneal cavity of into pelvic tissues along with other bacteria as a result of trauma, they cause suppuration (pus formation) and bacteremia.
  • coli a normal inhabitant of our gastro-intestinal tract causes urinary tract infection (UTI) if enters the urinary tract.
  • Hence, microbes of the normal resident flora are harmless and may be beneficial in their normal location in the host and in the absence of coincident abnormalities but they may produce disease if introduced into foreign location in large numbers and if predisposing factors are present.

Gnotobiontic animals:

  • Animals which are free from normal flora or which live in association with only certain known strains of bacteria and other microorganisms are called gnotobiontic animals.
  • When compared to animals having normal flora, these animals have poorly developed immune system and are more susceptible to infections caused by pathogenic microorganisms.
  • Gnotobiontic animals are used to study the effect of normal flora on the host.

Normal microbial flora and their Roles in the Human Body