WEB PAGE OF PADIYIL VINOD SIVADASAN

Bacterial Flora of Humans

Homeopathy

Drug  in Medical Emergencies

Anthrax

Brucellosis

Crimeancongo haemmorraghic fever

Leptospirosis

Rift Valley Fever 

Rabies

Feed back

The Bacterial Flora of Humans

In a healthy animal, the internal tissues, e.g. blood, brain, muscle, etc., are normally free of microorganisms. On the other hand, the surface tissues, e.g. skin and mucous membranes, are constantly in contact with environmental organisms and become readily colonized by certain microbial species. The mixture of organisms regularly found at any anatomical site is referred to as the normal flora.

The normal flora of humans is exceedingly complex and consists of more than 200 species of bacteria.  The makeup of the normal flora depends upon various factors, including genetics, age, sex, stress, nutrition and diet of the individual.  The normal flora of humans consists of a few eukaryotic fungi and protists, and some methanogenic Archaea that colonize the lower intestinal tract,  but the Bacteria are the most numerous and obvious microbial components of the normal flora.  The distribution of the bacterial flora of humans is shown in Table 1.  This table lists only a fraction of the total bacterial species that occur as normal flora of humans, and it does not express the total number or concentration of bacteria at any site.

Table 1 Notes

(1)  The staphylococci and corynebacteria occur at every site listed. Evidently, Staphylococcus epidermidis is the best adapted bacterium to its human host.  S. aureus is a potential pathogen. This bacterium is the leading cause of bacterial disease in humans.  It can be transmitted from the nasal membranes of an asymptomatic carrier to a susceptible host.

(2)  Many of the normal flora are either pathogens or opportunistic pathogens.  Besides a few notable pathogens that are not members of the normal flora (e.g. Mycobacterium tuberculosis), the asterisks indicate the most prevalent bacterial pathogens of humans.

(3) Streptococcus mutans is the primary bacterium involved in plaque formation and initiation of dental caries.  Viewed as an opportunistic infection, dental disease is one of the most prevalent and costly infectious diseases in the United States.

(4) Enterococcus faecalis was formerly classified as Streptococcus faecalis. The bacterium is such a regular a component of the intestinal flora, that many European countries use it as the standard indicator of fecal pollution, in the same way we use E. coli in the U.S.  In recent years, Enterococcus faecalis has emerged as a significant, antibiotic-resistant, nosocomial pathogen.

(5) Streptococcus pneumoniae is present in the upper respiratory tract of about half the population.  If it invades the lower respiratory tract it can cause pneumonia.  Streptococcus pneumoniae causes 95 percent of all bacterial pneumonia.

(6) Streptococcus pyogenes refers to the Group A, Beta-hemolytic streptococi.

(7) Gram-negative cocci, represented by various Neisseria, are frequent inhabitants of the upper respiratory tract, mainly the pharynx.  Neisseria meningitidis, an important cause of bacterial meningitis, can colonize as well, until the host can develop active immunity against the pathogen.

(8) While E. coli is a consistent resident of the small intestine, many other enteric bacteria may reside here as well, including Klebsiella, Enterobacter and Citrobacter.  Some strains of E. coli are pathogens that cause intestinal infections, urinary tract infections and neonatal meningitis.
 
(9) Pseudomonas aeruginosa is the quintessential opportunistic pathogen of humans that can invade virtually any tissue.  It is a leading cause of hospital-acquired (nosocomial) Gram-negative infections, but its source is often exogenous (from outside the host).

(10) Haemophilus influenzae is a frequent secondary invader to viral influenza, and was named accordingly.  The bacterium was the leading cause of meningitis in infants and children until the recent development of the Hflu type B vaccine.

(11) The greatest number of bacteria are found in the lower intestinal tract, specifically the colon and the most prevalent bacteria are the Bacteroides, a group of Gram-negative, anaerobic, non-sporeforming bacteria.  They have been implicated in the initiation colitis and colon cancer.
 
(12) Bifidobacterium bifidum is the Gram-positive counterpart to the Bacteroides in the colon.  They are anaerobic, non-sporeforming, lactic acid bacteria.  They are the "friendly" bacteria in the intestine.  Bacteroides predominate in the intestine of meat-eaters; bifidobacteria and other lactic acid bacteria predominate in the intestine of vegetarians.

(13)  Lactobacilli in the oral cavity probably contribute to acid formation that leads to dental caries.  Lactobacillus acidophilus colonizes the vaginal epithelium during child-bearing years and establishes the low pH that inhibits the growth of pathogens.

(14)  There are numerous species of Clostridium that colonize the bowel.  Clostridium perfringens is commonly isolated from feces.  Clostridium difficile may colonize the bowel and cause "antibiotic-induced diarrhea" or pseudomembranous colitis.

(15) Clostridium tetani is included in the table as an example of a bacterium that is "transiently associated" with humans as a component of the normal flora.  The bacterium can be isolated from feces of (up to) 25 percent of the population.  The endospores are probably ingested with food and water, and the bacterium does not colonize the intestine.

(16) The corynebacteria, and certain related propionic acid bacteria, are consistent skin flora.  Some have been implicated as a cause of acne.  Corynebacterium diphtheriae, the agent of diphtheria, was considered a member of the normal flora before the widespread use of the diphtheria toxoid, which is used to immunize against the disease.

Very little is known about the nature of the associations between humans and their normal flora, but they are thought to be dynamic interactions rather than associations of mutual indifference. Both host and bacteria are thought to derive  benefit from each other, and the associations are, for the most part, mutualistic.  The normal flora derives from the host a supply of nutrients, a stable environment and constant temperature, protection, and transport. The host obtains from the normal flora certain nutritional benefits, stimulation of the immune system, and colonization strategies that exclude potential pathogens at the site.

The normal flora are obviously adapted to their host (tissues), most probably by biochemical interactions between bacterial surface components (ligands or adhesins) and host cell molecular receptors. A great deal of information is available on the nature of adhesion of bacterial pathogens to animal cells and tissues, and reasonably similar mechanisms should apply to the normal flora.

In general, there are three explanations for why the normal bacterial flora are located at particular anatomical sites.
 

1. The normal flora exhibit a tissue preference or predilection for colonization. Certain species of bacteria are invariably in one locale and never in another (See Table 1 above). This is sometimes referred to as tissue tropism (See Table 2 below).  One explanation for tissue tropism is that the host provides an essential growth factor needed by the bacterium. Of course, to explain why bacteria are not at an alternative site, the host inherently provides an inhospitable environment for the bacterium by the production of such substances as stomach acids, bile salts and lysozyme.

2. Many, perhaps most, of the normal flora are able to specifically colonize a particular tissue or surface using their own surface components (e.g. capsules, fimbriae, cell wall components, etc.) as specific ligands for attachment to specific receptors located at the colonization site (See Table 3)

3. Some of the indigenous bacteria are able to construct bacterial biofilms on a tissue surface, or they are able to colonize a biofilm built by another bacterial species.  Many biofilms are a mixture of microbes, although one member is responsible for maintaining the biofilm and may predominate.

TABLE 2. EXAMPLES OF TISSUE TROPISM OF SOME BACTERIA

ASSOCIATED WITH HUMANS 

THE COMPOSITION OF THE NORMAL FLORA

The normal flora of corresponding anatomical sites in different animal species varies widely.  Within a single species (e.g. humans) there is additional variation in the normal flora that is related to factors such as age, sex, diet and nutrition.  Some bacteria are found regularly at particular anatomical locales; others are present only occasionally, or at certain times during life.  Developmental changes in humans such as weaning, the eruption of the teeth, and the onset and cessation of ovarian functions, invariably affect the composition of the normal flora in the intestinal tract, the oral cavity, and the vagina, respectively. However, within the limits of these fluctuations, the bacterial flora of humans is sufficiently constant to a give general description of the situation.

It has been calculated that the normal human houses about 10¹² bacteria on the skin, 10¹⁰ in the mouth, and 10¹⁴ in the gastrointestinal tract. The latter number is far in excess of the number of eukaryotic cells in all organs which comprise the human host.

Normal Flora of the Skin. The adult human is covered with approximately 2 square meters of skin. The density and composition of the normal flora of the skin vary with anatomical locale. The high moisture content of the axilla, groin, and areas between the toes supports the activity and growth of relatively high densities of bacterial cells, but the density of bacterial populations at most other sites is fairly low, generally in 100s or 1000s per square cm. Qualitatively, the bacteria on the skin near any body orifice may be similar to those in the orifice.

The majority of skin microorganisms are found in the most superficial layers of the epidermis and the upper parts of the hair follicles. They consist largely of micrococci (Staphylococcus epidermidis and Micrococcus sp.) and corynebacteria. These are generally nonpathogenic and considered to be commensal, although mutualistic and parasitic roles have been assigned to them. Sometimes potentially pathogenic Staphylococcus aureus is found on the face and hands, particularly in individuals who are nasal carriers.
 

Normal Flora of the Cunjunctiva. A variety of bacteria may be cultivated from the normal conjunctiva but the number of organisms is usually small. Staphylococcus epidermidis and certain coryneforms (Propoinibacterium acnes) are dominant. Staphylococcus aureus, some streptococci, Haemophilus sp. and Neisseria sp. are occasionally found. The conjunctiva is kept moist and healthy by the continuous secretions from the lachrymal glands. Blinking wipes the conjunctiva every few seconds mechanically washing away foreign objects including bacteria. Lachrymal secretions (tears) also contain bactericidal substances including lysozyme. There is little or no opportunity for microorganisms to colonize the conjunctiva without special mechanisms to attach to the epithelial surfaces and some ability to withstand attack by lysozyme. Pathogens which do infect the conjunctiva (e.g. Neisseria gonorrhoeae and Chlamydia trachomatis) are thought to be able to specifically attach to the conjunctival epithelium by means of sialic acid receptors on epithelial cells, but this is not certain.
 

Normal Flora of the Respiratory Tract. The nares (nostrils) are always heavily colonized, predominantly with Staphylococcus epidermidis and corynebacteria, and often (about 20% of the general population) with Staphylococcus aureus, this being the main carrier site of this important pathogen. The healthy sinuses, in contrast are sterile. A large number of bacterial species colonize the upper respiratory tract (nasopharynx). The predominant species are non-hemolytic and alpha-hemolytic streptococci and Neisseria, but sometimes pathogens such as Streptococcus pneumoniae, Streptococcus pyogenes, Haemophilus influenzae and Neisseria meningitidis colonize the pharynx.

The lower respiratory tract (trachea, bronchi, and pulmonary tissues) are virtually free of microorganisms, mainly because of the efficient cleansing action of the ciliated epithelium which lines the tract. Any bacteria reaching the lower respiratory tract are swept upward by the action of the mucociliary blanket that lines the bronchi, to be removed subsequently by coughing, sneezing, swallowing, etc. If the respiratory tract epithelium becomes damaged, as in bronchitis or viral pneumonia, the individual may become susceptible to infection by pathogens descending from the nasopharynx (e.g. H. influenzae or S. pneumoniae).  The pathogen Bordetella pertussis is specifically able to colonize the tracheal epithelium of humans, allowing it to produce the disease, pertussis (whooping cough).
 

Normal flora of the Urogenital Tract. Urine is normally sterile, and since the urinary tract is flushed with urine every few hours, microorganisms have problems gaining access and becoming established. The flora of the anterior urethra, as indicated principally by urine cultures, suggests that the area my be inhabited by a relatively consistent normal flora consisting of Staphylococcus epidermidis, Enterococcus faecalis and some alpha-hemolytic streptococci. Their numbers are not plentiful, however. In addition, some enteric bacteria (e.g. E. coli, Proteus) and corynebacteria, which are probably contaminants from the skin, vulva or rectum, may occasionally be found at the anterior urethra.

The vagina becomes colonized soon after birth with corynebacteria, staphylococci, nonpyogenic streptococci, E. coli, and a lactic acid bacterium historically named "Doderlein's bacillus" (Lactobacillus acidophilus). During reproductive life, from puberty to menopause, the vaginal epithelium contains glycogen due to the actions of circulating estrogens. Doderlein's bacillus predominates, being able to metabolize the glycogen to lactic acid. The lactic acid and other products of metabolism inhibit colonization by all except Doderlein's bacillus and a select number of lactic acid bacteria. The resulting low pH of the vaginal epithelium prevents establishment of most bacteria as well as the potentially-pathogenic yeast, Candida albicans. This is a striking example of the protective effect of the normal bacterial flora for their humam host.
 

Normal Flora of the Human Oral Cavity. The presence of nutrients, epithelial debris, and secretions makes the mouth a favorable habitat for a great variety of bacteria. Oral bacteria include streptococci, lactobacilli, staphylococci and corynebacteria, with a great number of anaerobes, especially bacteroides.

The mouth presents a succession of different ecological situations with age, and this corresponds with changes in the composition of the normal flora. At birth the oral cavity is composed solely of the soft tissues of the lips, cheeks, tongue and palate, which are kept moist by the secretions of the salivary glands. At birth the oral cavity is sterile but rapidly becomes colonized from the environment, particularly from the mother in the first feeding. Streptococcus salivarius is dominant and may make up 98% of the total oral flora until the appearance of the teeth (6 - 9 months in humans). The eruption of the teeth during the first year leads to colonization by S. mutans and S. sanguis. These bacteria require a nondesquamating (nonepithelial) surface in order to colonize. They will persist as long as teeth remain. Other strains of streptococci adhere strongly to the gums and cheeks but not to the teeth. The creation of the gingival crevice area (supporting structures of the teeth) increases the habitat for the variety of anaerobic species found. The complexity of the oral flora continues to increase with time, and Bacteroides and spirochetes colonize around puberty.

Clearly, the normal bacterial flora of the oral cavity benefit from their associations with their host. Are there benefits as well to the host? Perhaps. The normal flora occupy available colonization sites which makes it more difficult for other microorganisms (nonindigenous species) to become established. Also, the oral flora contribute to host nutrition through the synthesis of vitamins, and they contribute to immunity by inducing low levels of circulating and secretory antibodies that may cross react with pathogens. Finally, the oral bacteria exert microbial antagonism against nonindigenous species by production of inhibitory fatty acids, peroxides, bacteriocins, etc.

The oral flora of humans may harm their host since some of these bacteria are parasites or opportunistic pathogens. If certain oral bacteria are able to invade tissues not normally accessible to them, characteristic diseases result. For example, oral organisms gaining entrance into tissues (e.g. via surgical wounds) may cause abscesses of alveolar bone, lung, brain or the extremities. Such infections usually contain mixtures of bacteria with Bacteroides melaninogenicus often playing a dominant role. Also, oral streptococci may be introduced into wounds created by dental manipulation or treatment. If this occurs in an individual with damaged heart valves due to rheumatic fever (previously induced by streptococci), the oral streptococci may adhere to the damaged heart valves and initiate subacute bacterial endocarditis.
 

Dental Plaque, Dental Caries and Periodontal Disease

Dental plaque, dental caries and periodontal disease in humans also result from actions initiated by the normal bacterial flora. This is arguably the most significant and costly negative effect resulting from human symbioses with bacteria.

Dental Plaque, which is material adhering to the teeth, consists of bacterial cells (60-70% the volume of the plaque), salivary polymers, and bacterial extracellular products. Plaque is a naturally-constructed biofilm, in which the consortia of bacteria may reach a thickness of 300-500 cells on the surfaces of the teeth. These accumulations subject the teeth and gingival tissues to high concentrations of bacterial metabolites, which result in dental disease.

By far the dominant bacterial species in dental plaque are Streptococcus sanguis and Streptococcus mutans, both of which are considered responsible for plaque.

Plaque formation is initiated by a weak attachment of the streptococcal cells to salivary glycoproteins forming a pellicle on the surface of the teeth. This is followed by a stronger attachment by means of extracellular sticky polymers of glucose (glucans) which are synthesized by the bacteria from dietary sugars (principally sucrose). An enzyme on the cell surface of Streptococcus mutans, glycosyl transferase, is apparently involved in initial attachment of the bacterial cells to the tooth surface and in the conversion of sucrose to dextran and levan polymers (glucans) which form the extracellular matrix of plaque. Attachment of S. mutans and the formation of glucans is mediated by glycosyl transferase. The specificity of the adhesion has been proven by the fact that the attachment can be prevented by specific antibody to the enzyme.

Dental Caries is the destruction of the enamel, dentin or cementum of teeth due to bacterial activities. Caries are initiated by direct demineralization of the enamel of teeth due to lactic acid and other organic acids which accumulate in dental plaque. Lactic acid bacteria in the plaque produce lactic acid from the fermentation of sugars and other carbohydrates in the diet of the host. Streptococcus mutans has most consistently been associated with the initiation of dental caries, but other lactic acid bacteria are probably involved as well. These organisms normally colonize the occlusal fissures and contact points between the teeth, and this correlates with the incidence of decay on these surfaces.

Streptococcus mutans has a number of physiological and biochemical properties which implicate it in the initiation of dental caries.

1. It is a regular component of the normal oral flora of humans which occurs in relatively large numbers. It readily colonizes tooth surfaces: salivary components (mucins, which are glycoproteins) form a thin film on the tooth called the enamel pellicle. The adsorbed mucins are thought to serve as molecular receptors for ligands on the bacterial cell surface.

2. It contains the enzyme glycosyl transferase that probably serves as the bacterial ligand for attachment, and that polymerizes glucose obtained from dietary sucrose to glucans which leads directly to the formation of plaque.

3. It produces lactic acid from the utilization of dietary carbohydrate which demineralizes tooth enamel. S. mutans produces more lactic acid and is more acid-tolerant than most other streptococci.

4. It stores polysaccharides made from dietary sugars which can be utilized as reserve carbon and energy sources for production of lactic acid. The extracellular glucans formed by S. mutans are, in fact, bacterial capsular polysaccharides that function as carbohydrate reserves. The organisms can also form intracellular polysaccharides from sugars which are stored in cells and then metabolized to lactic acid.

Streptococcus mutans appears to be important in the initiation of dental caries because its activities lead to colonization of the tooth surfaces, plaque formation, and localized demineralization of tooth enamel. It is not however, the only cause of dental decay. After initial weakening of the enamel, various oral bacteria gain access to interior regions of the tooth. Lactobacilli, Actinomyces, and various proteolytic bacteria are commonly found in human carious dentin and cementum, which suggests that they are secondary invaders that contribute to the progression of the lesions.

Periodontal Diseases are bacterial infections that affect the supporting structures of the teeth (gingiva, cementum, periodontal membrane and alveolar bone). The most common form, gingivitis, is an inflammatory condition of the gums. It is associated with accumulations of bacterial plaque in the area. Increased populations of Actinomyces have been found, and they have been suggested as the cause.

Diseases that are confined to the gum usually do not lead to loss of teeth, but there are other more serious forms of periodontal disease that affect periodontal membrane and alveolar bone resulting in tooth loss. Bacteria in these lesions are very complex populations consisting of Gram-positive organisms (including Actinomyces and streptococci) and Gram-negative organisms (including spirochetes and Bacteroides). The mechanisms of tissue destruction in periodontal disease are not clearly defined but hydrolytic enzymes, endotoxins, and other toxic bacterial metabolites seem to be involved. 

 TABLE 4. FREQUENTLY ENCOUNTERED BACTERIA IN PLAQUE,

DENTAL CARIES, GINGIVITIS AND PERIODONTITIS 

Normal Flora of the Gastrointestinal Tract. The bacterial flora of the GI tract of animals has been studied more extensively than that of any other site. The composition differs between various animal species, and within an animal species. In humans, there are differences in the composition of the flora which are influenced by age, diet, cultural conditions, and the use of antibiotics.  The latter greatly perturbs the composition of the intestinal flora.  The following table shows the distribution of some common intestinal bacteria in various animal species including humans.
 

TABLE 5. NUMBERS OF VIABLE BACTERIA FOUND IN THE FECES OF

ADULT ANIMALS (Log # viable cells per gram feces) * 

In the upper GI tract of adult humans, the esophagus contains only the bacteria swallowed with saliva and food. Because of the high acidity of the gastric juice very few bacteria (mainly acid-tolerant lactobacilli) can be cultured from the normal stomach.  However, at least half the population in the United States is colonized by a pathogenic bacterium, Helicobacter pylori.  Since the 1980s, this bacterium has been known to be the cause of gastric ulcers, and it is probably a cause of gastric and duodenal cancer as well.
 
The proximal small intestine has a relatively sparse Gram-positive flora, consisting mainly of lactobacilli and Enterococcus faecalis.  This region has about 10⁵ - 10⁷ bacteria per ml of fluid. The distal part of the small intestine contains greater numbers of bacteria (10⁸/ml) and additional species including coliforms and Bacteroides, in addition to lactobacilli and enterococci. The flora of the large intestine (colon) is qualitatively similar to that found in feces. Populations of bacteria in the colon reach levels of 10¹¹/ml feces. Coliforms become more prominent, and enterococci, clostridia and lactobacilli can be regularly found, but the predominant species are anaerobic Bacteroides and anaerobic lactic acid bacteria in the genus Bifidobacterium (Bifidobacterium bifidum). These organisms may outnumber E. coli by 1,000:1 to 10,000:1. It is now known that significant numbers of anaerobic methanogenic bacteria (up to 10¹⁰/gm) also reside in the colon of humans. The range of incidence of certain bacteria in the large intestine of humans is shown below.
 

At birth the entire intestinal tract is sterile, but bacteria enter with the first feed. The initial colonizing bacteria vary with the food source of the infant. In breast-fed infants bifidobacteria account for more than 90% of the total intestinal bacteria. Enterobacteriaceae and enterococci are regularly present, but in low proportions, while bacteroides, staphylococci, lactobacilli and clostridia are practically absent. In bottle-fed infants, bifidobacteria are not predominant. When breast-fed infants are switched to a diet of cow's milk or solid food, bifidobacteria are progressively joined by enterics, bacteroides, enterococci lactobacilli and clostridia.  Apparently, human milk contains a growth factor that enriches for growth of bifidobacteria, and these bacteria play an important role in preventing colonization of the infant intestinal tract by non indigenous or pathogenic species.

The composition of the flora of the gastrointestinal tract varies along the tract (at longitudinal levels) and across the tract (at horizontal levels) where certain bacteria attach to the gastrointestinal epithelium and others occur in the lumen. There is frequently a very close association between specific bacteria in the intestinal ecosystem and specific gut tissues or cells (evidence of tissue tropism). Many bacteria adhere specifically to the gastrointestinal epithelial surfaces, and this has been shown in many animal species including humans, cows, dogs, pigs, mice and chickens. Gram-positive bacteria, such as the streptococci and lactobacilli, are thought to adhere to the gastrointestinal epithelium using polysaccharide capsules or wall lipoteichoic acids to attach to specific receptors on the epithelial cells. Likewise, Gram-negative bacteria such as the enterics may attach by means of specific fimbriae on the bacterial cell which bind to glycoproteins on the epithelial cell surface.
 

THE BENEFITS OF THE NORMAL FLORA

1. The normal flora synthesize and excrete vitamins in excess of their own needs, which can be absorbed as nutrients by the host. For example, enteric bacteria secrete Vitamin K and Vitamin B12, and lactic acid bacteria produce certain B-vitamins. Germ-free animals may be deficient in Vitamin K to the extent that it is necessary to supplement their diets.

2. The normal flora prevent colonization by pathogens by competing for attachment sites or for essential nutrients.  This is thought to be their most important beneficial effect, which has been demonstrated in the oral cavity, the intestine, the skin, and the vaginal epithelium.  In some experiments, germ-free animals can be infected by 10 Salmonella bacteria, while the infectious dose for conventional animals is near 10⁶ cells.

3. The normal flora may antagonize other bacteria through the production of substances which inhibit or kill nonindigenous species. The intestinal bacteria produce a variety of substances ranging from relatively nonspecific fatty acids and peroxides to highly specific bacteriocins, which inhibit or kill other bacteria.

4. The normal flora stimulate the development of certain tissues, i.e., the caecum and certain lymphatic tissues (Peyer's patches) in the GI tract. The caecum of germ-free animals is enlarged, thin-walled, and fluid-filled, compared to that organ in  conventional animals. Also, based on the ability to undergo immunological stimulation, the intestinal lymphatic tissues of germ-free animals are poorly-developed compared to conventional animals.

5. The normal flora stimulate the production of cross-reactive antibodies. Since the normal flora behave as antigens in an animal, they induce an immunological response, in particular, an antibody-mediated immune (AMI) response.  Low levels of antibodies produced against components of the normal flora are known to cross react with certain related pathogens, and thereby prevent infection or invasion.  Antibodies produced against antigenic components of the normal flora are sometimes referred to as "natural" antibodies, and such antibodies are lacking in germ-free animals.

Source: Kenneth Todar University of Wisconsin Department of Bacteriology