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The Normal Bacterial Flora of Humans (page 1)

(This chapter has 5 pages)

© Kenneth Todar, PhD

The Normal Flora

In a healthy animal, the internal tissues, e.g. blood, brain, muscle, etc., are normally free of microorganisms. However, the surface tissues, i.e., skin and mucous membranes, are constantly in contact with environmental organisms and become readily colonized by various microbial species. The mixture of organisms regularly found at any anatomical site is referred to as the normal flora, except by researchers in the field who prefer the term "indigenous microbiota". The normal flora of humans consists of a few eucaryotic fungi and protists, but bacteria are the most numerous and obvious microbial components of the normal flora.

Figure 1. Gram stain of a species of Micrococcus, commonly isolated from the skin and nasal membranes of humans.

The predominant bacterial flora of humans are shown in Table 1. This table lists only a fraction of the total bacterial species that occur as normal flora of humans. A recent experiment that used 16S RNA probes to survey the diversity of bacteria in dental plaque revealed that only one percent of the total species found have ever been cultivated. Similar  observations have been made with the intestinal flora.  Also, this table does not indicate the relative number or concentration of bacteria at a particular site. If you are reading online, you can skip this table and use it as an ongoing reference. To continue this article, scroll to the bottom of the Table notes to Associations Between Humans and the Normal Flora

Table 1. Bacteria commonly found on the surfaces of the human body.
Nose Pharynx Mouth Lower
Ant. ure-
Staphylococcus epidermidis (1) ++ + ++ ++ ++ + ++ ++
Staphylococcus aureus*  (2) +/- + + + ++ +/- +
Streptococcus mitis 

+ ++  +/-  + +
Streptococcus  salivarius 

++  ++   

Streptococcus mutans* (3)

+ ++

Enterococcus faecalis* (4)

+/-  + ++ + +
Streptococcus pneumoniae* (5)
+/-  +/-  + +

Streptococcus pyogenes* (6) +/- +/-
+ + +/-
Neisseria sp. (7)
+ ++  +
+ +
Neisseria meningitidis* (8)

+ ++ +

Enterobacteriaceae*(Escherichia coli) (9) 
+/-  +/- +/- + ++ + +
Proteus sp.
+/-  + + + + + +
Pseudomonas aeruginosa* (10)

+/-  +/- +/-
Haemophilus influenzae* (11)
+/-  +

Bacteroides sp.*

++  + +/-
Bifidobacterium bifidum (12)


Lactobacillus sp. (13)

+ ++ ++
Clostridium sp.* (14) 

+/-  ++

Clostridium tetani (15)


Corynebacteria (16) ++ + ++ + + + + +
Mycobacteria +
+/- +/- 



+ ++ ++


+ + + +/- +

++ = nearly 100 percent      + = common (about 25 percent)      +/- = rare  (less than 5%)       * = potential pathogen

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

    S. epidermidis. Scanning EM. CDC.

    (2)  Many of the normal flora are either pathogens or opportunistic pathogens, The asterisks indicate members of the normal flora a that may be considered major pathogens of humans.

    S. aureus. Gram stain.

    (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.

    Streptococcus mutans. Gram stain. CDC

    (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.

    Vancomycin Resistant Enterococcus faecalis. Scanning E.M. CDC

    (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.

    Streptococcus pneumoniae. Direct fluorescent antibody stain. CDC.

    (6) Streptococcus pyogenes refers to the Group A, Beta-hemolytic streptococci. Streptococci cause tonsillitis (strep throat), pneumonia, endocarditis. Some streptococcal diseases can lead to rheumatic fever or nephritis which can damage the heart and kidney.

    Streptococcus pyogenes. Gram stain.

    (7) Neisseria and other Gram-negative cocci 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.

    Neisseria meningitidis. Gram stain.

    (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.

    E. coli. Scanning E.M. Shirley Owens. Center for Electron Optics. Michigan State University.

    (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).

    Colonies of Pseudomonas aeruginosa growing on an agar plate. The most virulent Pseudomonas species produce mucoid colonies and green pigments such as this isolate.

    (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.

    Haemophilus influenzae. Gram stain.

    (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.

    Bacteroides fragilis. Gram stain.

    (12) Bifidobacteria are Gram-positive, non-sporeforming, lactic acid bacteria. They have been described as "friendly" bacteria in the intestine of humans. Bifidobacterium bifidum is the predominant bacterial species in the intestine of breast-fed infants, where it presumably prevents colonization by potential pathogens. These bacteria are sometimes used in the manufacture of yogurts and are frequently incorporated into probiotics.

    Bifidobacterium bifidum. Gram stain

    (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.

    Lactobacillus species and a vaginal squaemous epithelial cell. CDC

    (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.

    Clostridium perfringens. Gram stain.

    (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 in 0 - 25 percent of the population.  The endospores are probably ingested with food and water, and the bacterium does not colonize the intestine.

    Clostridium tetani. Gram stain.

    (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.

    Corynebacterium diphtheriae. No longer a part of the normal flora.

chapter continued

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Kenneth Todar has taught microbiology to undergraduate students at The University of Texas, University of Alaska and University of Wisconsin since 1969.

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