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Human normal microflora

Department of Microbiology Magorzata Prayska

Human normal microflora

The microbial population that colonizes the human body is numerous and diverse.
Colonization: permanent transient, for a short period such as hours or days These organisms do not produce disease in their normal setting but establish disease when they are introduced into unprotected sites (e.g., blood, tissues). If a patient's immune system is defective, that patient is more susceptible to disease caused by opportunistic pathogens.

Gram-positive bacteria coagulase-negative staphylococci Gram-negative bacteria do not permanently colonize the skin surface, because the skin is too dry do not multiply on the skin surface are easily removed

Corynebacterium spp.
Propionibacterium spp. Staphylococcus aureus

Bacillus spp.
Clostridium spp. Micrococcus spp.

Fungi Candida Malassezia

Outer ear
the most common organism colonizing the outer ear is coagulase-negative Staphylococcus other organisms colonizing the skin have been isolated from this site, as well as potential pathogens such as S. pneumoniae, Pseudomonas aeruginosa, and members of the Enterobacteriaceae family

Respiratory Tract
Mouth, Oropharynx, and Nasopharynx
the upper respiratory tract is colonized with numerous organisms 10 to 100 anaerobes for every aerobic bacterium most of these colonizers are relatively avirulent and are rarely associated with disease unless they are introduced into normally sterile sites (e.g., sinuses, middle ear, and brain)

Most common microbes that colonize the upper respiratory tract

Bacteria Acinetobacter Actinobacillus Actinomyces Cardiobacterium Corynebacterium Eikenella Enterobacteriaceae Eubacterium Fusobacterium Haemophilus Kingella Moraxella Fungi Candida Bacteria Mycoplasma Neisseria Peptostreptococcus Porphyromonas Prevotella Propionibacterium Staphylococcus Streptococcus Stomatococcus Treponema Veillonella Parasites Entamoeba Trichomonas

the surface of the eye is colonized with coagulase-negative staphylococci, as well as organisms found in the nasopharynx: Haemophilus spp., Neisseria spp., viridans streptococci

Lower respiratory tract

the larynx, trachea, bronchioles, and lower airways are sterile,
transient colonization with secretions of the upper respiratory tract may occur chronic aspiration may lead to a polymicrobial disease in which anaerobes are the predominant pathogen

Gastrointestinal tract
Esophagus oropharyngeal bacteria and yeast, as well as the bacteria that colonize the stomach, can be isolated from the esophagus however, most organisms are believed to be transient colonizers that do not establish permanent residence bacteria rarely cause disease of the esophagus (esophagitis)

Candida spp. and viruses such as herpes simplex virus and cytomegalovirus cause most infections

Gastrointestinal tract
the only organisms present are small numbers of acid-tolerant bacteria such as: the lactic acid-producing bacteria: Lactobacillus and Streptococcus spp. and Helicobacter pylori


Gastrointestinal tract
Small Intestine is colonized with many different bacteria, fungi, and parasites most of these organisms are anaerobes, such as Peptostreptococcus, Porphyromonas, and Prevotella spp.


Gastrointestinal tract
Large Intestine
more microbes are present in the large intestine than anywhere else in the human body

it is estimated that more than 1011 bacteria per gram of feces can be found, with anaerobic bacteria in excess by more than 1000-fold


Gastrointestinal tract
Large Intestine the most common bacteria include Bifidobacterium, Eubacterium, Bacteroides, Enterococcus, and the Enterobacteriaceae various yeasts can also establish residence in the large intestine. E. coli represents less than 1% of the intestinal population, it is the most common aerobic organism responsible for intraabdominal disease


Gastrointestinal tract
Large Intestine
Bacteroides fragilis is a minor member of the intestinal flora, but it is the most common anaerobe responsible for intraabdominal disease Eubacterium and Bifidobacterium are the most common bacteria in the large intestine but are rarely responsible for disease


Genitourinary system
the anterior urethra and vagina are the only anatomic areas of the genitourinary system permanently colonized with microbes the urinary bladder can be transiently colonized with bacteria migrating upstream from the urethra, these should be cleared rapidly by the bactericidal activity of the uroepithelial cells and the flushing action of voided urine the other structures of the urinary system should be sterile

Anterior urethra
the commensal population of the urethra consists of a variety of organisms, with lactobacilli, streptococci, and coagulasenegative staphylococci the most numerous

these organisms are relatively avirulent and are rarely associated with human disease
the urethra can be colonized transiently with fecal organisms such as Enterococcus, Enterobacteriaceae, and Candida-all of which can invade the urinary tract, multiply in urine, and lead to significant disease the isolation of N. gonorrhoeae or C. trachomatis in clinical specimens should always be considered significant, regardless of the presence or absence of clinical symptoms


lactobacilli - as the predominant organisms, and many other organisms are also isolated, including staphylococci (S. aureus less commonly than the coagulase-negative species), streptococci (including group B Streptococcus), Enterococcus, Gardnerella, Mycoplasma, Ureaplasma, Enterobacteriaceae, and a variety of anaerobic bacteria


Cervix and uterus

are not normally colonized with bacteria