Microbial ecology

Dr. Edet E. Udo

Department of Microbiology
Faculty of Medicine, Kuwait University.
 Microbial ecology
• Objectives:
• At the end of this session, students should:
• Define microbial ecology
• Discuss the different types of host- bacterial
relationship
• Discuss Normal flora and their nature and
significance at various body sites
• Discuss the habitats of common bacterial
pathogens
• Discuss biofilm and clinical significance of
biofilms
 Microbial ecology
• Definition:
• Ecology is the study of the relationship
between organisms and their environment.
• Types of relationships:
• Organisms relate to each other in a variety of
ways.
• Host: an organism that harbours another
organism.
• Symbiosis: the living together in close
association of two or more dissimilar
organisms.
• Commensalism
• ( eating at the same table): A relationship in
which one organism is neither harmed nor
helped while the other organism or population
gains. It is a non obligatory relationship.
• Commensal bacteria
• live in or on the host and benefits from it but
does not harm the host.
• Mutualism:
• a relationship in which both populations
benefit from the association. The host and the
mutualist are metabolically dependent.
• Chemotaxis helps bring organisms together
in a mutualistic relationship
 Microbial ecology
• Parasitism:
• A relationship that benefits on organism at
the expense of the other.
• Parasitic relationship are often very specific
e.g. Virus/host relationships.
• In parasitic relationship, the parasite gets a
suitable environment for growth.
• The host provides the parasite nutritional
needs either as food itself or the parasite uses
the host food or metabolic product.
• Parasitic organisms : (pathogens) bacteria,
viruses, fungi, plants, animals.
 Types of parasites
• Ectoparasites: on the surface of the
host
• Endoparasite: parasite lives inside the
host

Ectoparasites Endoparasites
• Pathogens:
– Microorganisms capable of causing disease
• Pathogenic microorganisms
• have special properties that allow them to
invade the human body or produce toxins.
• When the microorganisms overcomes the
body’s defenses, a state of disease results
• Disease: An abnormal state in which part or
all of the body is not properly adjusted or is
not capable of carrying out normal functions

• Infection is the invasion and and growth of

pathogens causing tissue injury.
 Types of pathogens:
• Primary pathogens :
• always associated with disease. E.g.
Mycobacterium tuberculosis, Neisseria
gonorrhoeae
• Opportunistic pathogens:
• Parts of the normal flora but becomes
pathogenic under certain situations. Examples
include E. coli, staphylococci, Pseudomonas
spp etc.
• Non pathogens: Not known to cause disease
• Contamination:
• the transient presence of microbes,
pathogenic or nonpathogenic, on the body
surfaces without any injury or invasion of
tissues
• Colonization:
• Continuing presence of microbes for extended
periods of time without causing injury or
invasion of tissue
 Normal flora
• Definition:
• Microorganisms that establish permanent
colonies inside or on the body without
producing disease.
• They are frequently found in particular sites
in normal healthy individuals.
• The composition and numbers of the flora
vary in different areas of the body and
sometimes at different age.
 Normal flora
• Normal flora can prevent pathogens from
causing an infection ( microbial antagonism)
• Normal flora and the host exist in a symbiotic
relationship
• It is estimated that a typical human body
contains 1 X 1013 cells yet harboura 1 X 1014
bacterial cells; the Large intestine contains >
100 billion bacteria
 Normal flora
The healthy fetus:
• is sterile until birth., later exposed to the flora
of the mother’s genital tract, to the skin and
respiratory flora of those handling it, and to
organisms in the environment
• Sterile body sites ( without normal flora):
• Blood, body fluids and tissues
• Transient flora
• Composed of microbes that are present for
various periods and then disappear.
• Occasional bacteria may be present briefly in
the bloodstream
• Transient bacteremia may be the source of
infections of damaged or abnormal valves that
leads to Subacute bacterial endocarditis
 Role of Normal flora
• 1. Infection resistance
– Occupy of binding sites on the surface of
human body cells and prevents the
attachment of pathogens to the same sites
– Mucin secretions- prevents attachment of
pathogenic organisms
– Secretion of noxious substances that may
be injurious to pathogenic bacteria

• 2. Stimulate the immune system:

– Normal flora, especially Gram-negative
rods, are strong immunogens.
– Because of cross-reactivity between related
bacteria , the antibodies produced in
response to commensal organisms confer
protection to the host from many
pathogenic organisms.
 Role of Normal flora

• 3. Act as nutrient source:

– Members of the normal flora provide
vitamin K, a cofactor essential for the
synthesis of clotting factors II, VII, and XI.
– Without this contribution from the normal
flora, the human clotting system would be
grossly ineffective
• 4. Stimulate epithelial cell turnover.
– Without normal flora, the gut would be thin
and without tone.
• Normal flora as pathogens:
• 1. Opportunistic infection by normal flora is a
common problem
• Immunocompromised host:
– In patients immunocompromised by
congenital defects, disease or therapy, a
wide variety of harmless microorganisms can
cause severe disease e.g AIDS patients.
Antibacterial therapy:
.Antibiotic- associated colitis caused by
Clostridium difficile and mucosal infections
caused by yeasts often follow antibiotic
administration and disturbance of the normal
flora.
 – Trauma: accidental or surgical trauma.
E.g. Postoperative abdominal abscesses and
posttraumatic peritonitis.
• 2. Bacterial translocation:
– the passage of viable bacteria from the
gastrointestinal tract through the epithelial
mucosa into the systemic circulation
• 3. Tissue invasion:.
– E.g. Streptococcus mutants, causes dental
caries by producing gelatinous deposits that
allow acid-producing bacteria to adhere to
the tooth enamel leading to the formation of
caries.
 Anatomic location of Normal
flora
• Body sites • Flora
• Skin, external ear, • Propionibacterium acnes,
distal urethra Staphylococcus
epidermidis,
diphtheroids,
Micrococcus spp, alpha-
and nonhaemolytic
streptococci
• Mouth, Tongue and
buccal mucosa • Viridans streptococci,
Neisseria species,
Branhamella , occasional
Candida albicans
• Nasopaharynx • Oral organisms, transient
• (URT) carriage of Streptococcus
pneumoniae, Haemophilus spp,
Neisseria meningitidis, oral
anaerobes.
• Stomach
• Rapidly becomes sterile after
meals
• Small intestine
• Scanty, variable and ill defined

• Mostly anaerobes: Bacteriodes

• Colon: Adults spp., Fusobacterium spp,
Clostridium spp,
Peptostreptococcus. Escherichia
coli, Proteus, other
Enterobactericeae,
Pseudomonas aeruginosa,
numerous other bacteria and
yeast
• Colon: • Bifidobacterium, lactobacilli,
aciduric streptococci
• During breast
feeding
• Lactobacilli, aciduric
• Vagina: streptococc, anaerobes,
yeasts

• Diptheroids (Corynebacterium
• Eye xerosis), Staphylococcus
epidermidis, non haemolytic
streptococci, Haemophilus
spp, Moraxella.
Concept of prebiotics and
probiotics
• The complex and balanced flora of the large
intestine prevents infection and and maintains
a positive effect on nutrition.

• Abrupt changes in diet, stress or antibiotic

therapy can upset the microbial balance and
render the host susceptible to diseases
• .
• The activities of health promoting flora in the
large intestine, preferably at the expense of
pathogens- can be improved through dietary
supplements.
 Concept of prebiotics and
• Prebiotics
probiotics
• are dietary components that have a specific
fermentation directed towards populations of
gut bacteria that are thought to be of benefit
to health.
• Prebiotics
• are defined as a non-digestible food
ingredient that affects the host by selectively
targeting the growth and / or activity of one or
a limited number of bacteria in the colon and
thus has the potential to improve host health.
• Examples are oligofructose and inulin which,
stimulates the growth of bifidobacteria in the
• Probiotics:
• The oral administration of living
microorganisms to promote health and growth.
They consist of lactobacilli, bifidobacteria ,
streptococci etc.
• Characteristics:
• adhere to host intestinal mucosa,
• are easily cultured, non pathogenic, non
toxic,
• produce useful enzymes or physiological end
products that benefits the host,
• remain viable for long periods and withstand
stomach acid and bile salts.
• How probiotics work to maintain
health (Mode of action):
– They compete with pathogens for nutrients
and adhesion sites
– Inactivate pathogenic bacterial toxins or
metabolites
– Produce substances that inhibits pathogens’
growth, stimulate non specific immunity
• Health benefits of probiotics:
– They have anticarcinogenic activity,
– control intestinal pathogens growth,
– improve lactose use in individuals with
lactose intolerance,
– reduce serum cholesterol.
 Microbial biofilms
• Biofilms are communities of microbes
associated with a surface such as pipes, soils,
medical implants and epithelial cells
• Biofilms can be composed of populations that
develop from a single species or a community
derived from multiple microbial species, and
they can form on a vast array of abiotic and
biotic surfaces
• Biofilm formation may require coordination
with, interactions of, and communication
between multiple bacterial species. .
Biofilm on Intravenous Catheter
Connecter 24 hours after Insertion
 Characteristics of biofilms
attached bacteria in disease
• Clinical biofilms infections are characterized
by symptoms that typically recur even after
repeated treatments with antibiotics.

• biofilms infections are rarely resolved by the

host's immune system.

• Biofilm bacteria release antigens and

stimulate the production of antibodies, yet
bacteria residing in biofilms are resistant to
these defense mechanisms
 Implant-Based ( Devise
-associated) Infections
• Bacterial biofilms on prosthetic valves are the
leading cause of endocarditis in patients who
have undergone heart valve replacement.
• The mortality rate among this group of
patients is as high as 70%
• Millions of catheters (e.g., central line,
intravenous, and urinary catheters)
• are inserted into patients every year, and
these implants serve as a potential surface for
biofilm formation.
 TABLE 1.   Examples of common implant infections
Associated disease or
Implant Organism(s) found
consequences
Prosthetic S. epidermidis, S. sanguis Prosthetic valve endoc
valve arditis
Contact P. aeruginosa, S. epidermidis Keratitis
lenses
Intravascular S. epidermidis, S. aureus Septicemia, endocardit
catheters is

Total artificial P. aeruginosa, S. epidermidis, Septicemia, device fail

heart S. aureus ure

Urinary E. coli, P. aeruginosa, Bacteriuria

catheters E. faecalis, Proteus mirabilis

Joint S. epidermidis, S. aureus Septicemia, device fail

replacement ure

Endotracheal P. aeruginosa, E. coli, Pneumonia

tube S. epidermidis, S. aureus

Voice Streptococci staphylococci Prosthesis failure

prostheses