NORMAL HUMAN

FLORA

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 HUMAN MICROBIOME
• The human microbiome (or human micro biota) is the
aggregate of microorganisms that reside on the surface
and in deep layers of skin, in the saliva and oral
mucosa, in the conjunctiva, and in the gastrointestinal
tracts. They include bacteria, fungi. Some of these
organisms perform tasks that are useful for the human
host. However, the majority have no known beneficial
or harmful effect. Those that are expected to be
present, and that under normal circumstances do not
cause disease, but instead participate in maintaining
health, are deemed members of the normal flora
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Normal flora vary in both number and kind from one
site to another.

Although, the normal flora extensively populate many

areas of the body, the internal organs such as CNS,
blood, liver, spleen, Kidneys and bladder are free of all
but the occasional transient organism.
 Types of skin Microbial flora

• There are two groups of normal flora:

1. Resident normal flora
2. Transient normal flora
• Resident normal floras
The resident flora consists of relatively fixed types of
microorganisms regularly found in a given area at a given
age; if disturbed, it promptly reestablishes itself
• Transient normal floras
are non-pathogenic or potentially pathogenic
microorganisms that inhabit the skin and mucus
membrane for a short period of time like hours,
days and weeks. It is derived from the environment
does not produce disease & does not establish itself
permanently on the surface.
 Normal flora can cause disease when:
• the defense mechanisms of the body
is breached
or
• when the micro-organism is placed in the
abnormal body site.
 SIGNIFICANCE OF NORMAL FLORA
• 1.The normal flora influences the anatomy, physiology,
susceptibility to pathogens, and morbidity of the host.

• 2. The effect of the normal flora on the host was not well
• understood until germ-free animals became available.
•

•
•

•
•
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 NORMAL BACTERIAL FLORA
• More bacterial than
human cells in the
body
• provide some nutrients
(vitamin K)
• stimulate immune system,
immunity can be
cross-reactive against
certain pathogens
• Prevent colonization by
potential pathogens

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 Significance of Normal Flora
Normal flora may aid the host in several ways:
• Aid in digestion of food
• Help the development of mucosa immunity
• Protect the host from colonization with
pathogenic microbes.
106
pathogenic GI infection
w/ normal flora microbes

10 pathogenic
microbes GI infection

w/ reduced flora after

Streptomycin treatment
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 OVERVIEW OF HUMAN-MICROBIAL
INTERACTIONS
• Microbial flora of the healthy human host
1) The reasons for understanding the normal flora of the healthy
human body
► Normal flora vs. human body
► Some normal flora: opportunistic pathogens
when injury occurred,
when resistance of body decreased,
when moved to another site

2) Origin of the normal flora

3) Relationship between normal flora and human host
4) Distribution and occurrence of the normal flora

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WHERE TO FIND MICROBE?
EVERYWHERE!

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 INTRODUCTION OF NORMAL
FLORA
1. A diverse microbial flora =>
• Human body Area: the skin and mucous membranes
• Time: shortly after birth until death
• Number: 1014 bacteria =>1013 host cells

• 2. Normal flora may:

• a. Aid the host
• b. Harm the host (in sometimes)
• c. Exist as commensals (no effect to the host)
3. Viruses and parasites => NOT normal microbial flora
• Most investigators consider that they are not commensals and
do not aid the host.

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 Normal Flora and
Pathogenesis

Colonization vs. Infection

Colonization: establishment of a site of reproduction of

microbes on a person without necessarily resulting in
tissue invasion or damage.
Infection: growth and multiplication of a microbe in or on
the body of the host with or without the production of
disease.
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 FACTORS INFLUENCING
NORMAL FLORA
1. Local Environment (pH,
temperature, O2, H2O,
and nutrient levels…).

2. Diet

3. Age

4. Health condition
(immune activity…)

5. Antibiotics,…..etc

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 COMPOSITION OF THE NORMAL FLORA
• The normal flora of humans are exceedingly complex and
consist of more than 200 species of bacteria.
• The makeup of the normal flora may be influenced by various
factors, including genetics, age, sex, stress, nutrition and diet of
the individual.
• Three developmental changes in humans, weaning, the
eruption of the teeth, and the onset and cessation of ovarian
functions, invariably affect the composition of the normal flora in
the intestinal tract, the oral cavity, and the vagina, respectively.
• However, within the limits of these fluctuations, the bacterial
flora of humans is sufficiently constant to a give general
description of the situation
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 NORMAL FLORA MAY ACT
AS OPPORTUNISTIC
PATHOGENS
• Especially in hosts
rendered susceptible by:

• 1. Immuno-suppression
(AIDS & SCID)

• 2. Radiation therapy &

Chemotherapy

• 3. Perforated mucous
membranes

• 4. Rheumatic heart
disease…etc.

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 WHEN WE GET COLONIZED WITH
NORMAL FLORA
• A human first becomes
colonized by a normal flora at
the moment of birth and passage
through the birth canal. In utero,
the fetus is sterile, but when the
mother's water breaks and the
birth process begins, so does
colonization of the body
surfaces. Handling and feeding
of the infant after birth leads to
establishment of a stable normal
flora on the skin, oral cavity and
intestinal tract in about 48 hours.

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A NEW BORN CHILD'S FLORA IS
DEPENDENT ON MOTHER
• The composition of a
child’s bacterial
flora is dependent
on the mother’s
micro flora, since
she is the primary
source for the
child’s bacteria at
the outset
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DENSITY OF NORMAL FLORA IN
HUMANS
• It has been calculated that a
human adult houses about 1012
bacteria on the skin, 1010 in the
mouth, and 1014 in the
gastrointestinal tract. The latter
number is far in excess of the
number of eukaryotic cells in all
the tissues and organs which
comprise a human..

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 HUMANS AS HABITATS
• Colonization (and infection) frequently begin at mucous
membranes
•These are found throughout the body. Consist of single or multiple layers of
epithelial cells, tightly packed cells in direct contact with the external
_____________________________.

Bacteria may
associate loosely
or firmly
Breaches in the

barrier can result

in infection
(pathogenesis)b
y opportunistic
pathogens 18
ASSOCIATIONS BETWEEN HUMANS AND THE
NORMAL FLORA
• E. coli is the best known
bacterium that regularly
associates itself with humans,
being an invariable component of
the human intestinal tract.
• Even though E. coli is the most
studied of all bacteria, and we
know the exact location and
sequence of 4,288 genes on its
chromosome, we do not fully
understand its ecological
relationship with humans

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 COMMENSAL RELATIONSHIP
• Sometimes the relationship between a
member of the normal flora an its host
cannot be deciphered.
• Such a relationship where there is no
apparent benefit or harm to either
organism during their association is
referred to as a commensal
relationship.
• Many of the normal flora that are not
predominant in their habitat, even
though always present in low
numbers, are thought of as
commensal bacteria.
• However, if a presumed commensal
relationship is studied in detail,
parasitic or mutualistic characteristics
often emerge.

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 NORMAL FLORA ARE MUTUALISTIC
• Much is not known about the nature of the associations between
humans and their normal flora, but they are thought to be
dynamic interactions.
• Both host and bacteria are thought to derive benefit from each
other, and the associations are, for the most part,
mutualistic.
• The normal flora derive from their host a steady supply of
nutrients, a stable environment, and protection and transport.
• The host obtains from the normal flora certain nutritional and
digestive benefits, stimulation of the development and activity of
immune system, and protection against colonization and
infection by pathogenic microbes.
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 Normal flora of the Skin
The skin is rich in resident bacterial flora, like:

• Coagulase negative Staphylococci(S.epidermidis)

• Diphtheroids
• Propionibacterium acne
• Peptostreptococci
• Alpha-hemolytic streptococci and non-hemolytic streptococci
• Staphylococcus aureus
• Non-pathogenic Neisseria sp.
• Factors that eliminating nonresident
microorganisms from the skin:
1) Low pH.
2) Lysozyme.
3) Fatty acids in sebaceous secretions.
 Important factors to keep skin
microbiota under control

1) Skin has a slightly acidic pH (4-6) due to organic

acids produced by staphylococci and secretions
from skin oil and sweat glands. The acidic pH
discourages colonization of many bacteria.
2) Lack of moisture drives many resident microbiota
into a dormant state. However in certain parts of
the body (scalp, ears and axillary areas) moisture is
sufficiently high to support a resident microbiota.
 Important factors to keep skin
microbiota under control

• Sweat of some parts of the skin contains a high concentration of

salt (sodium chloride). This makes the skin surface hyper-
osmotic which stresses most microorganisms.

• Lysozyme from sweat glands on the skin are bacterial inhibitory

substances. They help control of colonization, overgrowth and
infection from resident microorgsnisms.
 How skin microbiota keep their
population
• Neither profuse sweating nor washing and bathing
can eliminate or significantly modify the normal
resident flora.

• The number of superficial microorganisms may be

diminished by daily scrubbing with soap containing
hexachlorophene or other disinfectants, but the flora
is rapidly replenished again .
 Normal Flora of Respiratory Tract

• The upper respiratory tract is heavily colonized by normal flora.

• but the lower respiratory tract. (trachea, bronchi, bronchioles and

alveoli) do not have a normal microbiota (it is sterile) as they removed
by:

1. The continuous stream of mucus generated by the ciliated epithelial cells.

2. Phagocytic action of alveolar macrophages.

3. Lysozyme, which is present in nasal mucus has bactericidal effect

Respiratory Tract
Nose:
The flora of the Nose consists of:

• Staphylococcus aureus
• Staph.epidermidis
• Streptococci (Streptococcus pneumonia)
• Corynebacteria.
• Non pathogenic Neisseria
• Haemophilus sp.
Nasopharynx
• Some Neisseria species
• α-hemolytic Streptococci(S. pneumonia)
• Staphylococcus epidermidis
• Staphylococcus aureus
• Haemophilus influenzae
• Diphtheroids
• Branhamella catarrhalis
 Normal Flora of the Mouth

• The normal flora of the oral cavity contains

bacteria able to resist mechanical removal by
adhering to surface like the gum and teeth.
Those that can not attach are removed by the
mechanical flushing from the oral cavity to the
stomach where they are destroyed by
hydrochloric acid
• Sterile at birth
• after 4-12 hrs contaminated from birth canal with viridans
Streptococci (as resident flora remain so far life).

• Non-pathogenic Neisseria spp.like N. mucosa and N. lactamica

• Diphtheroids
• Anaerobes like Prevotella spp., Fusobacterium spp.
• Spirochetes
• Actinomyces
• Streptococci
• Veillonella(anaerobic G-ve cocci)

• (When teeth erupt) Rothia spp.(G+, pleomorphic aerobes).

 Normal Flora of the Intestinal Tract

• At birth is sterile.

• Newborns (in intensive care): the intestine colonized by

Enterobacteriaceae (Klebsiella, Citrobacter, Enterobacter).

• Breast-feed children:
- The initial residents of the colon of breast-fed infants are members
of the G+ve Bifidobacterium genus (G+, nonmotile, anaerobic
bacteria produce acid from carbohydrates & tolerate pH 5.) because
human milk contains a disaccharide amino sugar that
Bifidibacterium spp. require as a growth factor.

- Large No. of lactobacilli, lactic acid streptococci.

 • In formula-fed infants:
In formula-fed infants, Lactobacillus spp. predominate
because formula lacks the required growth factor.

• With the ingestion of solid food, these initial colonizers of

the colon are eventually displaced by a typical G-ve
microbiota.
Normal adult:
• Esophagus:
• In the normal adult, the esophagus contains microorganisms
arriving with saliva and food.

• Stomach:
acidity keeps the No. of microorganisms at minimum (103–105/g of
contents) unless obstruction at the pylorus favours the proliferation
of gram-positive cocci and bacilli.
Many microorganisms are washed from the mouth
into the stomach. Owing to the very acidic pH (2-3)
of the gastric contents, most m.o. are killed.
These are mainly:
Streptococcus
Staphylococcus
Lactobacillus
Peptostreptococcus
.
Some characteristics of stomach microbial flora

A) Some bacteria may survive if they rapidly pass through the stomach
or if those ingested with food are particularly resistant to gastric pH.

B) Normally the number of m.o. increase after a meal but quickly falls
as the acidic pH takes its role.

C) Changes in the gastric microbiota also occur if there is an increase in

gastric pH following intestinal obstruction, which permits a reflux of
alkaline duodenal secretions into the stomach.
Small intestine
• lactobacilli
• Diphtheroids
are occasionally found in the jejunum.
• In the distal part of the small intestine (ileum), the
microbiota begin to take the characteristics of the
colon microbiota. In the jejunum and ileum there are
about 105–108 bacteria/ gm of the contents.
• It is within the ileum that the pH becomes more
alkaline.
• As a result anaerobic G-ve bacteria and members of
the family Enterobacteriaceae become
established.
• The population size in the cecum and transverse
colon is about 108–1010 bacteria/gm and in the
sigmoid colon and rectum, there are about 1011
bacteria/gm of contents, constituting 10–30% of the
faecal mass.
Large intestine

The colon has the largest microbial population in the body.

Microscopic count of faeces approach 1012 organisms/gm wet
weight.

Over 300 species have been isolated from the human faeces. The
colon can be viewed as a large fermentation vessel, and
microbiota consists primarily of anaerobic, G-ve, non-sporing
rods.
Large intestine
- anaerobes (96-99% of resident flora):
- Fusobacterium spp.
- Bifidobacterium
- clostridia (C.dificile in small amount)
- anaerobic G+ cocci (Peptostreptococcus)
- facultative aerobes (1-4%) includes:
G- coliform
enterococci
small No. of
Pseudomonas,
lactobacilli,
Proteus .
 Normal Flora of the Genitourinary Tract

• The upper genitourinary tract (kidney, ureters,

and urinary bladder) is usually free of m.o. In
both the male and female

• a few bacteria such as :

Staphylococcus epidermidis
Enterococcus faecalis
Corynebacterium spp.
are usually present in the
distal part of the urethra.
Genitourinary Tract
Female
For anatomical reasons the female genital tract is much
more heavily colonized than that of the male and has a
complex microbiota that constantly changes with
maturation. The major m.o. are the acid-tolerant
lactobacilli, primarily Lactobacillus acidophilus.
 Normal Flora of the Eye

Bacteria found on conjunctiva of the eye are:

• Diphtheroids (Corynebacterium xerosis)

• Staphylococcus epidermidis
• Staphylococcus aureus
• Commensal Neisseria
• Streptococcus pneumonia
 Normal Flora of the Ear

• It is an extension of skin normal flora and often

profusely colonized.

• Staphylococcus epidermidis
• Diphtheroids
• Alpha-hemolytic and non-hemolyic
Streptococci

• Less frequently found are Bacillus and Neisseria

species.
 The role of Normal Flora

1) Synthesis of vitamin K in the gastrointestinal tract.

2) Absorption of nutrients & breakdown of products.

3) Prevent colonization by pathogenic micro-organisms and

possible disease through bacterial interference:
a. Competition for nutrition with pathogenic bacteria.
b. Competition for binding sites with pathogenic
bacteria.
4) Members of the normal flora may produce disease under
certain circumstances. For example, streptococci group are the
most common resident organisms of the upper respiratory tract.
They cause disease If large numbers of them are introduced into
the bloodstream (eg, following tooth extraction)

5) Microbial flora educate or train human immune system.