Microbiota of the human body.

Environmental microorganisms

Assoc. Prof. Dr. Tomas Kačergius

Institute of Biomedical Sciences, Faculty of Medicine
Vilnius University
 Human microbiome

• Microbiota of the human body is composed of ~100 trillion of prokaryotic and

eukaryotic microorganisms colonizing the skin and mucous membrane surfaces,
respiratory tract, digestive tract and genitourinary system.

• Microorganisms of the human microbiota have more than 5 million genes in

the whole, and this constitutes a “second genome” called the microbiome.

• In 2007, the National Institutes of Health (USA) initiated the Human Microbiome
Project in order to identify and characterized completely the microorganisms of
human microbiome as well as to determine its contribution to human health
and pathogenesis of diseases.

• Information about the Human Microbiome Project is available at:

http://nihroadmap.nih.gov/hmp/
 Microbiota of the human body

• The normal commensal population of microorganisms participates in the

metabolism of food products, provides essential growth factors, protects
against infections with highly virulent microorganisms, and stimulates
the immune response.

• Throughout the life of a human being, the microbial population continues

to change. Changes in health can drastically disrupt the delicate balance
that is maintained among the heterogeneous microorganisms coexisting
within us.

• Exposure of an individual to microorganisms can lead to one of three outcomes:

1) transient colonization of the person;
2) permanent colonization of the person;
3) production of the disease.
 Microbiota of the human body

• Microorganisms that colonize humans (whether for a short period or

permanently) do not interfere with normal body functions.

• Disease occurs when the interaction between microorganism and human leads
to a pathologic process characterized by damage to the human host.

• A few infections are caused by strict pathogens – microorganisms that are

always associated with human disease (e.g., Mycobacterium tuberculosis
[tuberculosis], Neisseria gonorrhoeae [gonorrhea]).

• Most human infections are caused by opportunistic pathogens – microorganisms

that are typically members of the human’s normal microbial flora (e.g.,
Escherichia coli, Candida albicans). These microorganisms do not produce
disease in their normal setting but establish disease when they are introduced
into unprotected sites (e.g., blood, tissues).
 Microbial flora of human skin

• Environment of skin does not support the survival of most microorganisms.

• Gram-positive bacteria (e.g., coagulase-negative Staphylococcus and, less

commonly, S. aureus, corynebacteria, and propionibacteria) are the most
common microorganisms found on the skin surface.

• Clostridium perfringens is isolated on the skin of approximately 20% of healthy

individuals, and the fungi Candida and Malassezia are also found on skin
surfaces, particularly in moist sites.

• Gram-negative rods with the exception of Acinetobacter are not commonly

cultured from the human skin.

• The Human Microbiome Project has revealed that uncultureable gram-

negative rods may be the most common microorganisms on the skin surface.
 Microbial flora of the ear and eye

• The most common microorganism colonizing the outer ear is coagulase-negative

Staphylococcus. Other microorganisms 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.

• The surface of the eye is colonized with coagulase-negative staphylococci, as

well as rare numbers of microorganisms found in the nasopharynx (e.g.,
Haemophilus spp., Neisseria spp., viridans streptococci). Disease is typically
associated with S. pneumoniae, S. aureus, H. influenzae, N. gonorrhoeae,
Chlamydia trachomatis, P. aeruginosa, and Bacillus cereus.
 Microbial flora of the upper respiratory tract

• Most of the common microorganisms in the upper respiratory tract are

relatively avirulent and are rarely associated with disease unless they are
introduced into normally sterile sites (e.g., sinuses, middle ear, brain).

• The most common bacteria are Streptococcus, Haemophilus, and Neisseria spp.

• Potentially pathogenic microorganisms, including Streptococcus pyogenes,

Streptococcus pneumoniae, S. aureus, Neisseria meningitidis, Haemophilus
influenzae, Moraxella catarrhalis, can also be found in the upper airways.
 Microbial flora of the lower respiratory tract

• The larynx, trachea, bronchioles, and lower airways are generally sterile,
although transient colonization with secretions of the upper respiratory tract
may occur.

• More virulent bacteria present in the nasopharynx (e.g., S. pneumoniae,

S. aureus, members of the family Enterobacteriaceae such as Klebsiella)
cause acute disease of the lower airway.

• Chronic aspiration may lead to a polymicrobial disease in which anaerobes

are the predominant pathogens, particularly Peptostreptococcus, related
anaerobic cocci, and anaerobic gram-negative rods.
 Microbial flora of the gastrointestinal tract

• Mouth:
700 species of microorganisms are identified, including bacteria, viruses and
yeast-like fungi. The predominant are streptococci (e.g., Streptococcus mutans)
and gram-negative anaerobic rods (e.g., Porphyromonas gingivalis). Most of the
identified microorganisms are uncultureable.

• Esophagus:
Oropharyngeal bacteria and yeast-like fungi, as well as the bacteria that
colonize the stomach, can be isolated from the esophagus. Bacteria rarely
cause disease of the esophagus (esophagitis); Candida spp. and viruses, such as
herpes simplex virus and cytomegalovirus, cause most infections.

• Stomach:
The only microorganisms present are small numbers of acid-tolerant bacteria,
such as the lactic acid-producing bacteria (Lactobacillus and Streptococcus spp.)
and Helicobacter pylori because the stomach contains hydrochloric acid and
pepsinogen. H. pylori is a cause of gastritis and ulcerative disease.
 Microbial flora of the gastrointestinal tract

• Small intestine:
It is colonized with many different bacteria and yeast-like fungi.
Most of these microorganisms are anaerobes, such as Peptostreptococcus,
Porphyromonas, and Prevotella. Common causes of gastroenteritis (e.g.,
Salmonella and Campylobacter spp.) can be present in small numbers as
asymptomatic residents; however, their detection in the clinical laboratory
generally indicates disease.

• Large intestine:
It is colonized with a large number of various different bacteria and yeast-like
fungi. The most common bacteria include Bifidobacterium, Eubacterium,
Bacteroides, Enterococcus, and the Enterobacteriaceae family. Escherichia coli
and Bacteroides fragilis are minor members of the intestinal flora, but they are
the most common causative agents of intraabdominal diseases. In contrast,
Eubacterium and Bifidobacterium are the most common bacteria in the large
intestine but are rarely responsible for disease. Antibiotic treatment can
rapidly alter the population, causing the proliferation of antibiotic-resistant
microorganisms, such as Enterococcus, Pseudomonas, and yeast-like fungi.
 Microbial flora of the genitourinary system

The anterior urethra and vagina are the only anatomic areas of genitourinary
system permanently colonized with microorganisms.

• Anterior urethra:
The commensal population of urethra consists of a variety of microorganisms,
with lactobacilli, streptococci, and coagulase-negative staphylococci the most
numerous. These microorganisms are relatively avirulent and are rarely
associated with human disease. The urethra can be colonized transiently with
fecal microorganisms, such as Enterococcus, Enterobacteriaceae, and Candida
– all of which can invade the urinary tract, multiply in urine, and lead to
significant disease. Pathogens such as N. gonorrhoeae and C. trachomatis are
common causes of urethritis and can persist as asymptomatic colonizers of
the urethra.
 Microbial flora of the genitourinary system
• Vagina:
The microbial population of the vagina is very diverse and is dramatically
influenced by hormonal factors. Newborn girls are colonized with lactobacilli at
birth, and these bacteria predominate for approximately 6 weeks. After that
time, the levels of maternal estrogen have declined, and vaginal flora changes
to include staphylococci, streptococci, and Enterobacteriaceae. When estrogen
production is initiated at puberty, the microbial flora again changes. Lactobacilli
reemerge as the predominant microorganisms, and many other microorganisms
are also isolated, including staphylococci (coagulase-negative species),
streptococci (including group B Streptococcus), Enterococcus, Gardnerella,
Mycoplasma, Ureaplasma, Enterobacteriaceae, and variety of anaerobic bacteria.
N. gonorrhoeae is a common cause of vaginitis. Trichomonas vaginalis,
C. albicans, and Candida glabrata are also important causes of vaginitis.
Herpes simplex virus and papillomavirus can also establish persistent infections.

• Cervix:
The cervix is not normally colonized with bacteria, however N. gonorrhoeae and
C. trachomatis are important causes of cervicitis. Actinomyces can also produce
disease at this site.
 Microorganisms in the air

• Air is not a natural environment for the microorganisms as it does not contain
enough moisture and nutrients to support their growth and reproduction. One
of the most common sources of air microbial flora is the soil.

• “The persistent” air microbial flora consists of mainly micrococci (e.g.,

Micrococcus flavus), Sarcina spp. (e.g., Sarcina alba) and fungal spores.

• The transient air microbial flora consists of the microorganisms that are
accidentally getting in the air by sneezing, coughing, talking and laughing in
the form of droplets. It can be pathogenic (e.g., influenza virus).

• The outdoor air is less microbiologically polluted than the indoor air (because
of the humans).

• The microbial pollution of the indoor air can be evaluated by counting the
total number of colony-forming units (CFU) in 1 m3 of the air. There should
not be found the pathogenic microorganisms (e.g., Mycobacterium tuberculosis).
 Microorganisms in the water

• Water can support the growth of many types of microorganisms.

• The persistent water microbial flora consists of specific aquatic aerobic

microorganisms like Pseudomonas fluorescens, Micrococcus roseus, etc.
Anaerobic bacteria are very rarely found in water.

• The transient water microbial flora consists of the microorganisms that are
accidentally getting in the water with faeces and urine. Those include very
pathogenic microorganisms like, for instance, salmonellae of enteric fever,
shigellae, leptospirae and Vibrio cholerae.

• The microbial pollution of the water can be evaluated by counting the total
number of colony-forming units (CFU) in 1 mL of the water. There should not
be found Escherichia coli and the pathogenic microorganisms (e.g., Salmonella
typhi, V. cholerae, etc.).
 Microorganisms in the soil

• Soil can support the growth of many types of microorganisms because it is rich
in nutrients.

• The persistent soil microbial flora consists of the nitrogen-fixing, denitrifying,

cellulose-splitting and sulfur bacteria, pigmented bacteria, fungi and protozoa.

• The transient soil microbial flora consists of the microorganisms that are
accidentally getting in the soil with faeces and urine (e.g., enterococci,
Clostridium perfringens). Also, the spores of clostridia causing tetanus,
anaerobic infections and botulism can be found in the soil.

• The microbial pollution of the soil can be evaluated by counting the total
number of colony-forming units (CFU) in 1 g of the soil.
 Microbial symbiosis

• The biological relationships between humans and microorganisms as well as

between microorganisms are defined as the symbiosis.

Types of the harmless Types of the antagonistic

symbiosis: symbiosis:

• Mutualism • Antibiosis
• Commensalism • Competition
• Metabiosis • Predation
• Satellitism • Parasitism
 Types of the harmless symbiosis

• Mutualism is any relationship between individuals where both individuals

benefit (e.g., human and its normal microbial flora).

• Commensalism is a relationship between two living organisms where one

benefits and the other is not significantly harmed or helped (e.g., human’s
normal microbial flora).

• Metabiosis is a relationship in which one microorganism creates or prepares

a suitable environment for the second (e.g., bacteria decompose proteins to
ammonia that is further oxidized to nitrous acid by the denitrifying bacteria).

• Satellitism is a relationship between bacteria in which certain bacterial species

grow more vigorously in the immediate vicinity of colonies of other unrelated
species, owing to the production of an essential metabolite by the latter species
(e.g., Staphylococcus aureus growing on the blood agar provides some factors
for the growth of Haemophilus influenzae).
 Types of the antagonistic symbiosis
• Antibiosis is an antagonistic relationship between two or more microorganisms
that is detrimental to at least one of them or an antagonistic relationship
between a microorganism and the metabolic substances produced by another
(e.g., the fungi of Penicillium genus produce penicillin, which is toxic to
bacteria).

• Competition is an antagonistic relationship where better adapted to environment

microorganisms utilize nutrients not leaving them to others (e.g., pathogenic
enterobacteria cannot survive long enough in the water due to the persistent
microbial flora of the water).

• Predation is an antagonistic relationship where microorganisms in association

“eat” other microorganisms (e.g., human intestinal amoebae “eat” enteric
bacteria).

• Parasitism is an antagonistic relationship between organisms, where one

individual, the parasite, benefits at the expense of the other, the host (e.g.,
relationship between strict pathogenic microorganisms and human; relationship
between virulent bacteriophages and bacteria).
 Literature

1. Black J. G., Black L. J. Microbiology: principles and explorations.

9th edition. Willey, New Jersey, 2015.

2. Murray P. R., Rosenthal K. S., Phaller M. A. Medical microbiology.

8th edition. Elsevier Inc., Philadelphia, 2015.