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Lecture 7
Normal Flora in Health and Disease

Normal Flora
In a healthy human, the internal tissues (e.g.
brain, blood, CSF, muscles) are normally free
of microorganisms
The surface tissues (e.g. skin and mucosa
membranes) are constantly in contact with
environmental microorganisms and become
readily colonised by various microbial species

Normal Flora
The mixture of microorganisms regularly
found at any anatomical site is referred to as
the normal microbiota (the indigenous
microbial population, the microflora, or the
normal flora)
Bacteria make up most of the normal
microbiota, they are emphasised over the
fungi (mainly yeast) and protists

Normal Flora
Reasons to acquire knowledge of normal
human microbiota:
An understanding of the different microorganisms
at particular locations provides greater insight into
the possible infections that might result from injury
to these body sites
A knowledge of the normal microbiota helps the
physician-investigator understand the causes and
consequences of colonisation and growth by
microorganisms normally absent at a specific body

Normal Flora
An increased awareness of the role that these
normal microbiota play in stimulating the host
immune response can be gained.
This awareness is important because the immune
system provides protection against potential

Normal Flora
Three of the most important types of
symbiotic relationships are commensalism,
mutualism, and parasitism
Within each category the association may be
either ectosymbiotic or endosymbiotic

Normal Flora
One of the most important functions of our
normal flora is to protect us from highly
pathogenic organisms.
For example, in a normal (bacterially inhabited
animal), about 106 Salmonella must be
ingested in order to cause disease.

Normal Flora
However, when an animal has been
maintained in a sterile environment all of its
life (a gnotobiotic animal), the same level of
disease can be produced by as few as 10
This dramatic difference is simply due to

Normal Flora
The normal commensal population of microbes
participates in the metabolism of food
products, provides essential growth factors,
protects against infections with highly virulent
microorganisms, and stimulates the immune
The human fetus lives in a protected, sterile
A newborn is exposed to microbes from others
and environment

Normal Flora
The infants skin is colonised first, followed by
the oropharynx, GI tract, and other mucosal
Throughout the life of an individual, this
microbial population continues to change
Changes in health can drastically disrupt the
delicate balance that is maintained among the
heterogeneous organisms coexisting within us

Normal Flora
Exposure of an individual to an organism can
lead to one of three outcomes
The organism can:
Transiently colonise the person
Permanently colonise the person
Produce disease

Disease Formation
The process can result from microbial factors:
e.g. damage to organs caused by the proliferation
of the microbe or the production of toxins or
cytotoxic enzymes)
or the hosts immune response to the organism

Strict pathogens (organism always associated

with diseases) - Mycobacteria tuberculosis,
Neisseria gonorrhea, Plasmodium sp.

Disease Formation
Opportunistic pathogens (organisms that are
typically members of the patients normal
flora) - Staphylococcus aureus, Escherichia coli,
Candida albicans
These organisms do not produce disease in
their normal setting but establish disease
when they are introduced into unprotected,
new sites

The adult human is covered with
approximately 2 m2 of skin
Commensal microorganisms living on or in the
skin can be either resident (normal) or
transient microbiota
Resident organisms normally grow on or in the
Their presence becomes fixed in well-defined
distribution patterns

Those that are temporarily present are
transient microorganisms
They usually do not become firmly entrenched
and are unable to multiply
Few microorganisms can penetrate the skin
because its outer layer consists of thick, closely
packed cells called keratinocytes
Continuous shedding of the outer epithelial
cells removes many of those microorganisms
adhering to the skin surface

The skin surface is not a favourable
environment for microbial colonisation - acidic
pH, high concentration of NaCl, lack of
moisture, and has certain inhibitory substances
Sweat glands release lysozyme (muramidase)
and cathelicidin (antimicrobial peptides)
Oil glands secrete complex lipids that may be
partially degraded by the enzymes from certain
Gram positive bacteria (e.g. Propionibacterium

These bacteria can change the secreted lipids
to unsaturated fatty acids which as oleic acid
that have strong antimicrobial activity against
Gram negative bacteria and some fungi
Some fatty acids are volatile and may be
associated with a strong odour
Most skin bacteria are found on superficial
cells, colonising dead cells, or closely
associated with the oil and sweat glands

Secretions from oil and sweat glands provide
the water, amino acids, urea, electrolytes, and
specific fatty acids that serve as nutrients
primarily for Staphylococcus epidermidis and
aerobic corynebacteria
Gram negative bacteria generally are found in
the more moist region
The yeasts Pityrosporum ovale and P.
orbiculare normally occur on the scalp

Nose and Nasopharynx

The normal microbiota of the nose is found
just inside the nostrils
S. aureus and S. epidermidis are predominant
bacteria present and are found in
approximately the same numbers as on the
skin of the surface

Nose and Nasopharynx

The nasopharynx, that part of the pharynx
lying above the level of the soft palate, may
contain small numbers of potentially
pathogenic bacteria such as Streptococcus
pneumoniae, Neisseria meningitidis, and
Haemophilus influenza
Diphtheroids, a large group of non-pathogenic
Gram positive bacteria that resemble
Corynebacterium, are commonly found in
both the nose and nasopharynx

At birth and throughout human life, a small
number of bacterial commensals are found on
the conjunctiva of the eye
The predominant bacterium is S. epidermis
followed by S. aureus, Haemophilus sp. and S.

External Ear
The normal microbiota of the external ear
resemble those of the skin, with coagulasenegative staphylococci and Corynebacterium
Fungi: Aspergillus, Alternaria, Penicillium,
Candida, and Saccharomyces

The normal microbiota of the mouth or oral
cavity contains organisms that resist mechanical
removal by adhering to surfaces like the gums
and teeth
The continuous desquamation (shedding) of
epithelial cells also removes microorganisms
Those microorganisms able to colonise the
mouth find a very comfortable environment due
to the availability of water and nutrients, the
suitability of pH and temperature, and the
presence of many other growth factors

The oral cavity is colonised by microorganisms
from the surrounding environment within
hours after a human is born
Most microorganisms that invade the oral
cavity initially are aerobes and obligate
anaerobes (Porphyromonas, Prevotella, and
Fusobacterium) become dominant due to the
anoxic nature of the space between the teeth
and gums

As the teeth grow, Streptococcus parasanguis
and Streptococcus mutans attach to their
enamel surfaces
Streptococcus salivarius attaches to the buccal
and gingival epithelial surfaces and colonises
the saliva
The presence of these bacteria contributes to
the eventual formation of dental plaque,
caries, gingivitis, and periodontal diseases

Owing to the very acidic pH (2 - 3) of the
gastric contents, most microorganisms are
Less than 10 viable bacteria / mL of gastric
Streptococcus, Staphylococcus, Lactobacillus,
Peptostreptococcus, and yeasts such as
Candida sp.

Small Intestine
The duodenum contains few microorganisms
because of the combined influence of the
stomachs acidic juices and the inhibitory action
of the bile and pancreatic secretions
Gram positive cocci and rods comprise most of
the microbiota
Jejunum - Enterococcus faecalis, lactobacilli,
diphtheroids, and Candida albicans
Ileum - pH becomes more alkaline; anaerobic
Gram negative bacteria and members of the
family Enterobacteriaceae become established

Large Intestine
Has the largest microbial community in the
body (>400 different species; many exist in
large number)
The microbiota consist primarily of anaerobic,
Gram negative bacteria and Gram positive,
spore-forming, and non-sporing rods
Several studies have shown that the ration of
anaerobic to facultative anaerobic bacteria is
approximately 300 to 1

Large Intestine
Yeast (Candida albicans) and certain protozoa
may occur as harmless commensals
Trichomonas hominis, Entamoeba hartmanni,
Endolimax nana, and Iodomoeba butschlii are
common inhabitants
Bacteriodes thetaiontaomicron suits for
survival in the gut, where it is able to degrade
complex dietary polysaccharides

Large Intestine
Methanogenic bacteria are thought to remove
the products of fermentation by converting H2
and CO2 to methane
Various physiological processes move the
microbiota through the colon so an adult
eliminates about 3 x 10 microorganisms daily peristalsis and desquamation of the surface
epithelial cells

Large Intestine
To maintain homeostasis of the microbiota,
the body must continually replace lost
The bacterial population in the human colon
usually doubles once or twice a day
Under normal conditions the resident
microbial community is self-regulating

Large Intestine
Competition and mutualism between different
microorganisms and between the
microorganisms and their host serve to
maintain a status quo
If the intestinal environment change, the
normal microbiota may change greatly
Disruptive factors: stress, altitude change,
starvation, parasitic organisms, diarrhoea, and use
of antibiotics or probiotics

Genitourinary Tract
The upper genitourinary tract (kidneys,
ureters, and urinary bladder) is usually free of
In both female and male, a few bacteria (S.
epidermidis, Enterococcus faecalis, and
Corynebacterium sp.) usually are present in
the distal portion of the urethra

Genitourinary Tract
The adult female genital tract because of its
large surface area and mucous secretions, has
a complex microbiota that constantly changes
the females menstrual cycle
The major microorganisms are the acidtolerant lactobacilli (Lactobacillus acidophilus
or Dderleins bacillus) vaginal pH: 4.4. 4.6

The Relationship between Normal

Microbiota and the Host
After a microorganism enters or contacts a
host, a positive mutually beneficial
relationship occurs that becomes integral to
the health of the host
These microorganism become the normal
The microorganism produces or induces
deleterious effects on the host; the end result
may be disease or even death of the host

The Relationship between Normal

Microbiota and the Host
Some microorganisms are pathogens
They are prevented from causing disease by
competition provided by the normal
The normal microbiota use space, resources,
and nutrients needed by pathogens
They may produce chemicals that repel
invading pathogens

The Relationship between Normal

Microbiota and the Host
These microbiota prevent colonisation by
pathogens and possible disease through
bacterial interference
Products made by colonic bacteria (e.g.
Vitamin B and K) also benefit the host
Studies using germ-free animals suggest a
strong correlation between the establishment
of stable microbial flora and the induction of
immune competency

The Relationship between Normal

Microbiota and the Host
The induction of normal faecal flora to germfree rodents stimulates the production and
secretion of angiogenin-4, an antimicrobial
peptide of intestinal Paneth cells
The reconstitution of germ-free rodents with
flora from conventially raised siblings causes
the abnormal gut-associated lymphoid tissue
and intestinal lamina propria to resemble that
of the conventional animals

The Relationship between Normal

Microbiota and the Host
Although normal microbiota offer some
protection from invading pathogens, they may
themselves become pathogenic and produce
disease under certain circumstances, and then
are term opportunistic microorganisms or
The opportunistic microorganisms are
adapted to the non-invasive mode of life
defined by the limitations of the environment
in which they are living

The Relationship between Normal

Microbiota and the Host
For example, streptococci of the viridans
group are the most common resident bacteria
of the mouth and oropharynx
If they are introduced into the bloodstream in
large numbers, they may settle on deformed
or prosthetic heart valves and cause
Opportunistic microorganisms often cause
disease in compromised hosts

The Relationship between Normal

Microbiota and the Host
There are many causes of this condition
including malnutrition, alcoholism, cancer,
diabetes, leukaemia, another infectious
disease, trauma from surgery or an injury, an
altered normal microbiota from the prolonged
use of antibiotics, and immunosuppression by
various factors (e.g. drugs, viruses, hormones
and genetic deficiencies)

The Relationship between Normal

Microbiota and the Host
Normal microbiota are harmless and are often
beneficial in their normal location in the host
and in the absence of coincident
However, they can produce disease if
introduced into foreign locations or
compromised hosts

Microbes and Infection

These microbes colonised the body, but they
remain in the outer surfaces without
penetrating into sterile tissues or fluids
When a microbe has penetrated the host
defenses, invaded sterile tissues, and
multiplied INFECTION!
Invasion by most microorganisms begins when
they adhere to cells in a persons body

Microbes and Infection

Symptoms of disease are determined by the
function of tissue affected, although systemic
responses, produced by toxins, and host
defense responses may also occur
The seriousness of the symptoms depends on
the importance of the organ affected and the
extend of the damage caused by the infection

Microbes and Infection

The bacterial strain and inoculum size are also
major factors in determining whether disease
occurs; however, this can vary from a
relatively small inoculum to a very large

Pathogenicity of Microbes and Virulence

Adherence is a very specific process, involving
lock-and-key connections between the
microorganism and cells in the body
Some microorganisms that invade the body
produce toxins
Some diseases are caused by toxins produced
by microorganisms outside the body

Pathogenicity of Microbes and Virulence

After multiplication begins, one of three
things can happen:
Microorganisms continue to multiply and
overwhelm the bodys defenses
A state of balance is achieved, causing chronic
The body - with or without medical treatment destroys and eliminates the invading

Pathogenicity of Microbes and Virulence

Whether the microorganism remains near the
invasion site or spreads to other sites depends
on such factors as whether it produces toxins,
enzymes, or other substances
Pathogenic action:
Tissue destruction
Endotoxin and cell wall components

Pathogenicity of Microbes and Virulence

1. Tissue destruction
By products of bacterial growth, especially
fermentation result in the production of acids,
gas, and other substances that are toxic to tissue
Many bacteria release degradative enzymes to
breakdown the tissue, thereby providing food for
the growth of the organisms and promoting the
spread of the organisms, especially if blood
vessels are involved

Pathogenicity of Microbes and Virulence

2. Toxin
Bacterial components that directly harm tissue or
trigger destructive biological activities
Cause lysis of cells, and specific receptor-binding
proteins that initiate toxic reactions in a specific
target tissue or initiate a systematic response (e.g.
fever) by promoting the inappropriate release of

Pathogenicity of Microbes and Virulence

3. Endotoxin and other cell wall components
Peptidoglycan and its breakdown products, as well
as teichoic and lipoteichoic acids are released, and
these stimulate toxin-like pyrogenic acute-phase
Lipopolysaccharide produced by Gram -ve bacteria is
an even more powerful activator of acute-phase and
inflammatory reaction
Endotoxin binds to specific receptors on
macrophages, B cells, and other cells and stimulates
the production and release of acute-phase cytokines

Pathogenicity of Microbes and Virulence

Endotoxin also stimulates the growth (mitogenic) of B
At low concentration, endotoxin stimulates the
mounting of protective responses such as fever,
vasodilation, and the activation of the immune and
inflammatory responses
High concentration of endotoxin activate the
alternative pathway of complement and promote
high fever, hypotension, shock produced by
vasodilation and capillary leakage, and disseminated
IV coagulation stemming from the activation of the
blood coagulation pathways

Pathogenicity of Microbes and Virulence

4. Exotoxins
Proteins that can be produced by bacteria and
induce cytolytic enzymes and receptor-binding
proteins that alter the function or kill the cell
In many cases, the toxin gene is encoded on a
plasmid or a lysogenic phage
Super-antigens are a special group of toxins
These molecules activate T cells by binding
simultaneously to a T-cell receptor - life threatening
autoimmune-like responses by stimulating the
release of large amounts of interleukins

Pathogenicity of Microbes and Virulence

5. Immunopathogenesis
The symptoms of a bacterial infection are
produced by excessive immune and inflammatory
responses triggered by the infection
The acute-phase response to cell wall
components, especially endotoxin, is an initial
phase of the protective antibacterial response but
can also cause the life threatening symptoms
associated with sepsis and meningitis

Bacteria (Infection and Colonisation)

Infection: local or systemic infection
Local infection - limited to specific part of the
body where the microorganisms remain
Systemic infection - microorganisms spread and
damage different part of the body

When a culture of the persons blood reveals

microorganisms BACTERAEMIA
When bacteraemia results in systemic

Bacteria (Infection and Colonisation)

Infection that appear suddenly or last a very
short time acute infection
Infection that occurs slowly, over a very long
period, and may last months or years
chronic infection

Bacteria (Infection and Colonisation)

Infection in a wound is indicated by the
appearance of inflammation and pus
The patient may become pyrexial, and wound
swab will indicate the presence of large
numbers of causative organisms

Bacteria (Infection and Colonisation)

When colonisation occurs, several species of
bacteria may be present, often referred to as
mixed bacterial growth on laboratory reports
Colonisation is of clinical significance because
the organism may multiply in large numbers to
form a reservoir
Colonisation is usually the precursor to infection
when outbreaks occurs, and even if the original
patient escapes the clinical signs and symptoms
of disease, cross-infection may still occur

Overview of Bacterial Pathogenesis

1. Maintain a reservoir. A reservoir is a place to live
and multiply before and after causing an infection
2. Initial transport to and entry into the host
3. Adhere to, colonise, and/or invade host cells or
4. Multiply or complete its life cycle on or in the
host or the hosts cells
5. Damage the host
6. Leave the host and return to the reservoir or
enter a new host

Gaining Access
1. Inhalation
Through respiratory tract (nose or mouth), aerosols,
droplet transmission
The longer the period of exposure, the greater the
risk of inhalation
e.g. influenza virus

2. Ingestion
Through mouth into gastrointestinal tract
e.g. food poisoning, typhoid fever
e.g. of causative agents: Salmonella, Shigella, E. coli,
Vibrio and the virus causing poliomyelitis enter by
being ingested

Bacterial Adherence Factors that Play a

Role in Infectious Diseases
Adherence Factor



Filamentous structures that help attach bacteria to other

bacteria or to solid surfaces

Glycocalyx or capsule

A layer of exopolysaccharide fibers with a distinct outer

margin that surrounds many cells; it inhibit phagocytosis and
aids in adherence. When the layer is well organised and not
easily washed off, it is called a capsule


Filamentous structures that bind prokaryotes together for

the transfer of genetic material

S Layer

The outermost regularly structured layer of cell envelopes of

some bacteria that may promote adherence to surfaces

Slime Layer

A bacterial film that is less compact than a capsule and is

removed easily

Teichoic and
lipoteichoic acids

Cell wall components in Gram +ve bacteria that aid in


Invasion of Host Tissues

Pathogens often actively penetrate the hosts
mucous membranes and epithelium after
attachment to the epithelial surface
This may be accomplished through production
of lytic substances that alter host tissue by:
Attacking the extracellular matrix and basement
membranes of integuments and intestinal linings
Degrading carbohydrate-protein complexes
between cells or on the cell surface (glycocalyx)
Disrupting the cell surface

Microbial Defenses Against Host

Immunologic Clearance

Antigenic mimicry
Antigenic masking
Antigenic shift
Production of antiimmunoglobulin
6. Destruction of

7. Inhibition of
8. Inhibition of
9. Inhibition of
phagolysosome fusion
10. Resistance to
lysosomal enzymes
11. Intracellular

Leaving the Host

The last determinant of a successful bacterial
pathogen is its ability to leave the host and
enter either a new host or a reservoir
Unless a successful escape occurs, the disease
cycle will be interrupted and the
microorganism will not be perpetuated
Passive escape occurs when a pathogen or its
progeny leave the host in faeces, urine,
droplets, saliva, or desquamated cells

i) Normal flora
ii) Opportunistic organisms
iii) Pathogenic organisms
iv) Bacteraemia
v) Septicaemia


Name the normal flora on skin, respiratory

tract, digestive tract and urinary tract.


What are the bacterial pathogenic actions?