A healthy newborn enters the world in essentially sterile condition, but, after birth, it rapidly acquires

normal flora from food and the environment, including from other humans.

The human microbiome is the total number and diversity of microbes found in and on the human body.

In the past, the ability to cultivate organisms from tissues and clinical samples was the gold standard for

identification of normal flora and bacterial pathogens.

However, the recent application of culture-independent molecular detection methods based on DNA

sequencing indicates that the human body contains a far greater bacterial diversity than previously

recognized.

Unlike classic microbiologic culture methods, molecular detection requires neither prior knowledge of an

organism nor the ability to culture it. Thus, molecular methods are capable of detecting fastidious and

nonculturable species. Even using advanced molecular techniques, it is difficult to define the human

microbiome because microbial species present vary from individual to individual as a result of

physiologic differences, diet, age, and geographic habitat. Despite these limitations, it is useful to be

aware of the dominant types and distribution of resident flora, because such knowledge provides an

understanding of the possible infections that result from injury to a particular body site.

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Section I– Microbiology Introductory By Dr. Mohammed Ayad

Microbial Flora

The most common sites of the body inhabited by normal flora are, as might be expected, those in contact

or communication with the outside world, namely, the skin, eye, and mouth as well as the upper

respiratory, gastrointestinal, and urogenital tracts.

I- Skin can acquire any bacteria that happen to be in the immediate environment, but this transient

flora either dies or is removable by washing. Nevertheless, the skin supports a permanent bacterial

population (resident flora), residing in multiple layers of the skin. The resident flora regenerates even

after vigorous scrubbing.

Estimate of the skin microbiome using classical culture techniques: Staphylococcus epidermidis and other

coagulase-negative staphylococci (CON) that reside in the outer layers of the skin appear to account for

some 90 % of the skin aerobes. Anaerobic organisms, such as Propionibacterium acnes, reside in deeper

skin layers, hair follicles, and sweat and sebaceous glands.

Skin inhabitants are generally harmless, although S. epidermidis can attach to and colonize plastic

catheters and medical devices that penetrate the skin, sometimes resulting in serious bloodstream

infections.

While estimate of the skin microbiome using molecular sequencing techniques: The estimate of the

number of species present on skin bacteria has been radically changed by the use of the 16S ribosomal

RNA gene sequence to identify bacterial species present on skin samples directly from their genetic

material.

Previously, such identification had depended upon microbiological culture, upon which many varieties of

bacteria did not grow and so were not detected. Staphylococcus epidermidis and Staphylococcus aureus

were thought from culture-based research to be dominant. However DNA analysis research finds that,

while common, these species make up only 5 % of skin bacteria. The skin apparently provides a rich and

diverse habitat for bacteria.

II- Eye

The conjunctiva of the eye is colonized primarily by S. epidermidis, followed by S. aureus, aerobic

Corynebacteria (diphtheroids), and Streptococcus pneumoniae. Tears, which contain the antimicrobial

enzyme lysozyme, help, limit the bacterial population of the conjunctiva.

III- Buccal cavity and Nasal passages

The mouth and nose harbor many microorganisms, both aerobic and anaerobic. Among the most common

are diphtheroids (aerobic Corynebacterium species), S. aureus, and S. epidermidis. In addition, the teeth

and surrounding gingival tissue are colonized by their own particular species, such as Streptococcus

mutans.

S. mutans can enter the bloodstream following dental surgery and colonize damaged or prosthetic heart

valves, leading to potentially fatal infective endocarditis.

Some normal residents of the nasopharynx can also cause disease like S. pneumoniae, found in the

nasopharynx of many healthy individuals, can cause acute bacterial pneumonia, especially in older adults

and those whose resistance is impaired ((Pneumonia is frequently preceded by an upper or middle

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Section I– Microbiology Introductory By Dr. Mohammed Ayad

respiratory viral infection, which predisposes the individual to S. pneumoniae infection of the

pulmonary parenchyma))

IV- Gastrointestinal tract

In an adult, the density of microorganisms in the stomach is relatively low (103

to 105

per gram of

contents) due to gastric enzymes and acidic pH.

The density of organisms increases along the alimentary canal, reaching 108

to 1010 bacteria per gram of

contents in the ileum and 1011 per gram of contents in the large intestine.

Some 20 % of the fecal mass consists of many different species of bacteria, more than 99 % of which are

anaerobes. Bacteroides species constitute a significant percentage of bacteria in the large intestine.

Escherichia coli, a facultative anaerobic organism, constitutes less than 0.1 % of the total population of

bacteria in the intestinal tract. However, this endogenous E. coli is a major cause of urinary tract

infections (UTIs).

V- Urogenital tract

The low pH of the adult vagina is maintained by the presence of Lactobacillus species, which are the

primary components of normal flora. If the Lactobacillus population in the vagina is decreased (for

example, by antibiotic therapy), the pH rises, and potential pathogens can overgrow.

The most common example of such overgrowth is the yeast-like fungus, Candida albicans which itself is

a minor member of the normal flora of the vagina, mouth, and small intestine. The urine in the kidney

and bladder is sterile but can become contaminated in the lower urethra by the same organisms that

inhabit the outer layer of the skin and perineum.

Normal flora benefits

Normal flora can provide some definite benefits to the host:

First, the sheer number of harmless bacteria in the lower bowel and mouth make it unlikely that, in a

healthy person, an invading pathogen could compete for nutrients and receptor sites.

Second, some bacteria of the bowel produce antimicrobial substances to which the producers

themselves are not susceptible.

Third, bacterial colonization of a newborn infant acts as a powerful stimulus for the development of

the immune system.

Fourth, bacteria of the gut provide important nutrients, such as vitamin K, and aid in digestion and

absorption of nutrients; although humans can obtain vitamin K from food sources, bacteria can be an

important supplemental source if nutrition is impaired.

Microbial flora problems

Clinical problems caused by normal flora arise in the following ways:

The organisms are displaced from their normal site in the body to an abnormal site. An example is

the introduction of the normal skin bacterium, S. epidermidis, into the bloodstream where it can colonize

catheters and heart valves, resulting in bacterial endocarditis.

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Section I– Microbiology Introductory By Dr. Mohammed Ayad

Potential pathogens gain a competitive advantage due to diminished populations of harmless

competitors; when normal bowel flora are depleted by antibiotic therapy leading to overgrowth by the

resistant Clostridium difficille , which can cause severe colitis.

Harmless, commonly ingested food substances are converted into carcinogenic derivatives by

bacteria in the colon; like the conversion by bacterial sulfatases of the sweetener cyclamate into the

bladder carcinogen cyclohexamine.

When individuals are immunocompromised, normal flora can overgrow and become pathogenic

((Colonization by normal, but potentially harmful, flora should be distinguished from the carrier state in

which a true pathogen is carried by a healthy (asymptomatic) individual and passed to other individuals

where it results in disease)). Typhoid fever is an example of a disease that can be acquired from a

carrier

Microorganism’s pathogenesis

A pathogenic microorganism is defined as one that is capable of causing disease. Some microorganisms

are unequivocally pathogenic, whereas others (the majority) are generally harmless.

An organism may invade an individual without causing infectious disease when the host’s defense

mechanisms are successful.

The occurrence of such asymptomatic infections can be recognized by the presence of antibody against

the organism in the patient’s serum. Some infections result in a latent state, meaning that the organism is

dormant but may be reactivated with the recurrence of symptoms. Moreover, some pathogens cause

disease only under certain conditions (for example, being introduced into a normally sterile body site or

infection of an immunocompromised host).

Bacterial mediated pathogenesis

The mechanism of infectious process may vary among bacteria, the methods by which bacteria cause

disease can, in general, be divided into several stages. Pathogenicity of a microorganism depends on its

success in completing some or all of these stages. The terms “virulence” and “pathogenicity” are often

used interchangeably. However, virulence can be quantified by how many organisms are required to cause

disease in 50 percent of those exposed to the pathogen (ID50, where I = Infectious and D = Dose), or to

kill 50 percent of test animals (LD50, where L = Lethal).

The number of organisms required to cause disease varies greatly among pathogenic bacteria, as less than

100 Shigella cause diarrhea by infecting the gastrointestinal (GI) tract, whereas the infectious dose of

Salmonella is approximately 100,000 organisms.

The infectious dose of a bacterium depends primarily on its virulence factors. The probability that an

infectious disease occurs is influenced by both the number and virulence of the infecting organisms and

the strength of the host immune response opposing infection.