Normal microbial flora, now commonly referred to as normal microbiota, are the populations of microorganisms that inhabit the skin and mucous membranes of healthy individuals.
These microorganisms play beneficial roles including:
Acting as a first line of defense against microbial pathogens.
Assisting in digestion of food.
Degrading toxins in the body.
Contributing to the development and maturation of the immune system.
Disturbances or shifts in the normal microbiota or inflammation triggered by commensal microbes may contribute to diseases such as inflammatory bowel disease (IBD).
Various bacteria and fungi are permanent residents of specific body sites including the skin, oropharynx, colon, and vagina.
Viruses and parasites, the other two major groups of microorganisms, are usually not considered part of the normal flora, although they may be present in asymptomatic individuals.
The skin and mucous membranes always harbor a variety of microorganisms, which can be categorized into two types:
Resident flora: Consists of relatively stable and consistent microorganisms regularly found in a particular area at a certain age. If disrupted, it tends to reestablish quickly.
Transient flora: Comprises nonpathogenic or potentially pathogenic microorganisms that temporarily inhabit the skin or mucous membranes for a few hours to weeks. These are usually environment-derived, do not cause disease, and do not permanently colonize the host.
As long as the resident flora is intact, transient flora generally pose little risk. However, if resident flora is disturbed, transient organisms may proliferate and lead to infections or diseases.
Organisms that make up the normal flora are often referred to as commensals.
Commensals are organisms that benefit from the host without causing harm.
While the normal flora extensively populates external-facing body sites, the internal organs and fluids are typically sterile.
Body fluids such as blood, cerebrospinal fluid (CSF), lymph, urine, and semen are normally free of microorganisms.
Internal organs including the central nervous system, lower bronchi and alveoli, liver, spleen, kidneys, and bladder are devoid of microorganisms, except for occasional transient organisms that do not establish colonization.
Role of the Resident Microbiota
The growth of microflora on or inside the body depends on physiological factors such as temperature, moisture, availability of nutrients, and the presence of inhibitory substances.
The resident microbiota in certain body areas plays an important role in maintaining health and normal physiological functions.
In the intestinal tract, some members of the resident flora:
Synthesize vitamin K.
Aid in the absorption of nutrients.
On mucous membranes and skin, resident flora may prevent the colonization of pathogenic microorganisms and reduce the risk of disease through a process called bacterial interference.
Bacterial interference mechanisms include:
Competition for receptors or binding sites on host cells.
Competition for nutrients needed for microbial growth.
Mutual inhibition by metabolic by-products or toxic substances.
Inhibition by bacteriocins or naturally produced antibiotics.
Other protective mechanisms not yet fully understood.
If the normal microflora is disturbed (due to antibiotics, illness, or other factors), the area can be repopulated by organisms from the external environment or from other parts of the body.
These new organisms may act as opportunistic pathogens and potentially cause disease.
Competitive Protective Role of Microflora
Members of the normal microbiota may also cause disease under certain conditions.
These organisms are typically adapted to a noninvasive mode of life, restricted by the environment in which they reside.
If removed from their normal environment and introduced into the bloodstream or deep tissues, they may become pathogenic.
For example:
Viridans group streptococci are common residents of the upper respiratory tract.
If introduced into the bloodstream (e.g., after tooth extraction or oral surgery), they may colonize deformed or prosthetic heart valves and cause infective endocarditis.
Even minor trauma like dental scaling or vigorous brushing can introduce small numbers of these bacteria transiently into the blood.
Bacteroides species, which are dominant in the large intestine, are harmless in that location.
However, if they are introduced into the peritoneal cavity or pelvic tissues along with other bacteria due to trauma, they can cause bacteremia.
The normal resident microbiota are usually harmless or beneficial in their natural location within the host and in the absence of abnormalities.
They can cause disease if they enter foreign body sites, especially in large numbers and when predisposing conditions exist.
The skin, the largest human organ, is colonized by a diverse microbiota, most of which are harmless or beneficial.
Due to constant environmental exposure, the skin also frequently hosts transient microorganisms.
Despite this, the skin maintains a well-defined resident flora, which may vary in different anatomical areas due to:
Secretions,
Wearing of clothes, and
Proximity to mucous membranes (e.g., mouth, nose, and perineal region).
Normal flora of skin
The predominant organism on the skin is Staphylococcus epidermidis, a nonpathogenic bacterium under normal conditions that can transcend its harmless role and cause disease when introduced into sterile sites such as prosthetic joints or artificial heart valves.
S. epidermidis is found on the skin far more frequently than its pathogenic counterpart, Staphylococcus aureus.
There are approximately 10³ to 10⁴ organisms/cm² of skin, forming a verdant microbial layer over our body.
While most organisms are located superficially, some delve into the labyrinth of hair follicles, acting as a reservoir to replenish the surface flora after hand washing.
Anaerobic organisms, such as Propionibacterium and Peptococcus, reside in the deeper dermal follicles, where the oxygen tension is low, forming a crucible of microbial adaptation.
Propionibacterium acnes, a common anaerobe, is notably implicated in the pathogenesis of acne, orchestrating inflammation in these low-oxygen sanctuaries.
The predominant resident microorganisms of the skin include a rich mosaic of:
Staphylococcus epidermidis
Staphylococcus aureus (in small numbers)
Micrococcus species
α-Hemolytic and nonhemolytic streptococci (e.g., Streptococcus mitis)
Corynebacterium species
Propionibacterium species
Peptostreptococcus species
Acinetobacter species
And small numbers of other enigmatic organisms, such as Candida species and Pseudomonas aeruginosa, which occasionally embark on pathogenic roles under the right conditions.
Normal Flora of Oral Cavity
Streptococcus mutans, a member of the viridans group, is abundant in dental plaque and plays a key role in the development of dental caries (tooth decay).
This plaque forms on the enamel surface and is made up of gelatinous glucans secreted by the bacteria.
The trapped bacteria within the plaque produce significant amounts of acid, which leads to enamel demineralization and initiates caries formation.
Viridans streptococci are also the primary cause of subacute bacterial (infective) endocarditis.
These organisms can enter the bloodstream during dental procedures and attach to damaged heart valves, causing infection.
Anaerobic bacteria, such as Fusobacterium and Clostridium species, thrive in the gingival crevices, where oxygen levels are very low.
If these anaerobes are aspirated into the lungs, especially in patients with poor dental hygiene, they can lead to lung abscesses.
The gingival crevices are also the natural habitat of Actinomyces israelii, an anaerobic actinomycete that can cause abscesses in the jaw, lungs, or abdominal cavity.
Normal Flora of Upper Respiratory Tract
The nose, throat, and mouth are colonized by a wide variety of microorganisms, while the lower bronchi and alveoli usually contain few or no organisms.
The nose harbors several streptococcal and staphylococcal species, with Staphylococcus aureus being the most clinically significant pathogen.
S. aureus colonization in the nose can lead to disease outbreaks, especially in newborn nurseries, and often originates from nasal or skin colonization in healthcare workers.
The throat is home to viridans streptococci, Neisseria species, and Staphylococcus epidermidis.
These nonpathogenic organisms occupy mucosal binding sites in the pharynx, thereby inhibiting colonization by pathogens such as:
Streptococcus pyogenes
Neisseria meningitidis
Staphylococcus aureus
Normal Flora of Digestive Tract
In healthy fasting individuals, the stomach contains very few microorganisms, mainly due to its acidic (low pH) environment.
The small intestine typically harbors small populations of microbes such as streptococci, lactobacilli, and yeasts—especially Candida albicans.
These microbial numbers increase in the terminal ileum.
The colon is the primary site of bacterial colonization in the body, with bacteria making up about 20% of fecal mass.
Over 90% of the colonic flora are anaerobic bacteria, with Bacteroides fragilis being the most significant.
Among facultative anaerobes, Escherichia coli is the most prevalent species.
The intestinal microbiota also influences disease processes beyond the gut.
For example, E. coli is the primary causative agent of urinary tract infections (UTIs).
Antibiotic therapy (e.g., with clindamycin) can disrupt the normal gut flora, enabling overgrowth of less common organisms such as toxin-producing Clostridium difficile, which may result in severe colitis.
Oral administration of certain antibiotics (e.g., neomycin) before gastrointestinal surgery is used to reduce bacterial load ("sterilize" the gut).
This leads to a temporary suppression of normal flora for several days, after which microbial populations gradually recover.
Normal flora of Genitourinary Tract
In adult women, the vaginal microbiota is dominated by Lactobacillus species.
These bacteria help inhibit the growth of potential pathogens by maintaining an acidic environment.
When lactobacilli are reduced (e.g., due to antibiotic use), it can lead to Candida albicans overgrowth, causing Candida vaginitis.
The proximity of the vagina to the anus makes it susceptible to colonization by fecal flora.
Approximately 15–20% of women of reproductive age carry group B streptococci in the vagina.
This bacterium can be transmitted to newborns during delivery, potentially causing neonatal sepsis and meningitis.
Around 5% of women harbor Staphylococcus aureus in the vagina.
This colonization may predispose them to toxic shock syndrome, especially in the presence of risk factors (e.g., tampon use).
In healthy individuals, urine within the bladder is sterile.
However, during urination, it may become contaminated by microorganisms from the distal urethra such as:
Coliforms
Staphylococcus epidermidis
Diphtheroids
The external genital skin may host Staphylococcus saprophyticus, a significant cause of urinary tract infections in women.
