Download Microbial ecology and biotechnology

Microbial ecology and
biotechnology
Dr. Mohammad Shakeeb ,MD
Specialist in clinical
pathology/microbiology and
immunology
INTRODUCTION
• The science of ecology is the systematic study of the
interrelationships that exist between organisms and
their environment.
• Microbial ecology is the study of the numerous
interrelationships between microorganisms and the
world around them.
• Most relationships between humans and microbes
are beneficial rather than harmful.
• Microorganisms interact with humans in many ways
and at many levels.
INTRODUCTION
• The most intimate association that we have with
microorganisms is their presence both on and within
our bodies.
• Additionally, microbes play important roles in
agriculture, various industries, disposal of industrial
and toxic wastes, sewage treatment, and water
purification.
• Microbes are essential in the fields of biotechnology,
bioremediation, genetic engineering, and gene
therapy.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• Symbiosis
• is defined as the living together or close association
of two dissimilar organisms (usually two different
species).
• Symbionts: the organisms that live together in such a
relationship.
• Mutualistic relationships : are beneficial to both
symbionts.
• commensalistic relationships : are beneficial to only
one symbiont.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• parasitic relationships : are harmful to one symbiont.
Neutralism
• The term neutralism is used to describe a symbiotic
relationship in which neither symbiont is affected by
the relationship.
Commensalism
• A symbiotic relationship that is beneficial to one
symbiont and of no consequence (i.e., is neither
beneficial nor harmful) to the other.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• Many of the organisms in the indigenous microflora
of humans are considered to be commensals.
• Tiny mite called Demodex, which lives within hair
follicles and sebaceous glands, especially those of
the eyelashes and eyebrows.
Mutualism
• Mutualism is a symbiotic relationship that is
beneficial to both symbionts (i.e., the relationship is
mutually beneficial).
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• An example is the intestinal bacterium Escherichia
coli, which obtains nutrients from food materials
ingested by the host and produces vitamins (such as
vitamin K) that are used by the host.
• Vitamin K is a blood-clotting factor that is essential to
humans.
• Some members of our indigenous microflora prevent
colonization by pathogens and overgrowth by
opportunistic pathogens.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
Parasitism
• Parasitism is a symbiotic relationship that is
beneficial to one symbiont (the parasite) and
detrimental to the other symbiont (the host).
• Trypanosoma gambiense—is the parasite that causes
African sleeping sickness, a human disease that often
causes death of the host.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• A change in conditions can cause one type of
symbiotic relationship to shift to another type.
• Conditions can cause a mutualistic or commensalistic
relationship between humans and their indigenous
microflora to shift to a parasitic, disease-causing
(pathogenic) relationship.
• many of the microbes of our indigenous microflora
are opportunistic pathogens (opportunists), awaiting
the opportunity to cause disease.
SYMBIOTIC RELATIONSHIPS
INVOLVING MICROORGANISMS
• Conditions that may enable an opportunist to cause
disease include burns, lacerations, surgical
procedures, or diseases that debilitate (weaken) the
host or interfere with host defense mechanisms.
• Immunosuppressed individuals are especially
susceptible to opportunistic pathogens.
• Opportunists can also cause disease in otherwise
healthy persons if they gain access to the blood,
urinary bladder, lungs, or other organs and tissues of
those individuals.
INDIGENOUS MICROFLORA
OF HUMANS
INDIGENOUS MICROFLORA
OF HUMANS
• A person’s indigenous microflora or
indigenous
microbiota
(sometimes
referred to as “normal flora”) includes
all of the microbes (bacteria, fungi,
protozoa, and viruses) that reside on
and within that person
INDIGENOUS MICROFLORA
OF HUMANS
• A fetus has no indigenous microflora.
• During and after delivery, a newborn is exposed to
many microorganisms from its mother, food, air, and
virtually everything that touches the infant.
• Both harmless and helpful microbes take up
residence on the:
 baby’s skin
 body openings
 mucous membranes
INDIGENOUS MICROFLORA
OF HUMANS
• These moist, warm environments provide excellent
conditions for growth.
• types of resident flora differ from one anatomic site
to another.
• Blood, lymph, spinal fluid, and most internal tissues
and organs are normally free of microorganisms.
• They are sterile
INDIGENOUS MICROFLORA
OF HUMANS
• When the number of usual resident microbes is
greatly reduced, opportunistic invaders can more
easily establish themselves within those areas.
• Candida albicans is the yeast, important opportunist
usually found in small numbers near body openings.
• in the absence of sufficient numbers of other
resident microflora, may grow unchecked.
• causing the disease candidiasis (also known as
moniliasis).
INDIGENOUS MICROFLORA
OF HUMANS
• Such an overgrowth or population explosion
of an organism that is usually present in low
numbers is referred to as a superinfection.
INDIGENOUS MICROFLORA
OF HUMANS
Microflora of the Skin
• The most common bacteria on the skin are species of
Staphylococcus (especially S. epidermidis and other
coagulase-negative staphylococci), Corynebacterium, and
Propionibacterium.
• Moist, warm conditions in hairy areas of the body where
there are many sweat and oil glands, such as under the arms
and in the groin area, stimulate the growth of many different
microorganisms.
INDIGENOUS MICROFLORA
OF HUMANS
• moist folds between the toes and fingers support many
bacteria and fungi.
• The surface of the skin near mucosal openings of the body
(the mouth, eyes, nose, anus, and genitalia) is inhabited by
bacteria present in various excretions and secretions.
• most infections after burns, wounds, and surgery result from
the growth of resident or transient skin microflora in these
susceptible areas.
• Healthcare professionals must be particularly careful to keep
their skin and clothing as free of transient microbes as
possible to help prevent personal infections and to avoid
transferring pathogens to patients.
INDIGENOUS MICROFLORA
OF HUMANS
Microflora of the Ears and Eyes
• The middle ear and inner ear are usually sterile
• outer ear and the auditory canal contain the same types of
microorganisms as are found on the skin.
• When a person coughs, sneezes, or blows his or her nose,
these microbes may be carried along the eustachian tube and
into the middle ear where they can cause infection.
• Infection can also develop in the middle ear when the
eustachian tube does not open and close properly.
INDIGENOUS MICROFLORA
OF HUMANS
• The external surface of the eye is lubricated, cleansed, and
protected by tears, mucus, and sebum.
• Continual production of tears and the presence of the enzyme
lysozyme and other antimicrobial substances found in tears
greatly reduce the numbers of indigenous microflora
organisms found on the eye surfaces.
INDIGENOUS MICROFLORA
OF HUMANS
Microflora of the Respiratory Tract
• The nasal passages and throat have an abundant and varied
population of microorganisms.
• Some people—known as healthy carriers— harbor virulent
(disease-causing) pathogens in their nasal passages or throats,
but do not have the diseases associated with them.
• carriers can transmit them to susceptible persons.
• The lower respiratory tract is usually free of microbes.
INDIGENOUS MICROFLORA
OF HUMANS
Microflora of the Oral Cavity (Mouth)
• Both aerobic and anaerobic.
• Anaerobic microorganisms flourish in gum margins, crevices
between the teeth, and deep folds (crypts) on the surface of
the tonsils.
• Bacteria thrive especially well in particles of food and in the
debris of dead epithelial cells around the teeth.
• Carelessness in dental hygiene allows growth of these
bacteria.
• development of dental caries (tooth decay), gingivitis (gum
disease), and more severe periodontal diseases.
INDIGENOUS MICROFLORA
OF HUMANS
• The most common organisms in the indigenous microflora of
the mouth are various species of α-hemolytic streptococci.
• The bacterium most often implicated in the formation of
plaque is Streptococcus mutans.
INDIGENOUS MICROFLORA
OF HUMANS
• Microflora of the Gastrointestinal Tract
• the GI tract includes the esophagus, stomach, small intestine,
large intestine (colon), and anus.
• Gastric enzymes and the extremely acidic pH (approximately
pH 1.5) of the stomach usually prevent growth of indigenous
microflora .
• There is one bacterium—a Gram-negative bacillus named
Helicobacter pylori—that lives in some people’s stomachs and
is a common cause of ulcers.
• many are found in the lower parts of the small intestine (the
jejunum and ileum).
INDIGENOUS MICROFLORA
OF HUMANS
• The colon contains the largest number and variety of
microorganisms of any colonized area of the body.
• Because the colon is anaerobic, the bacteria living there are
obligate, aerotolerant, and facultative anaerobes.
• Actinomyces, Bacteroides, Clostridium, Enterobacter,
Enterococcus, Escherichia, Klebsiella, Lactobacillus, Proteus,
Pseudomonas, Staphylococcus, and Streptococcus.
• opportunists, causing disease only when they gain access to
other areas of the body.
INDIGENOUS MICROFLORA
OF HUMANS
• Microflora of the Genitourinary Tract
• Consists of the urinary tract (kidneys, ureters, urinary bladder,
and urethra) and the various parts of the male and female
reproductive systems.
• The healthy kidney, ureters, and urinary bladder are sterile.
• distal urethra and the external opening of the urethra harbor
many microbes, including bacteria, yeasts, and viruses.
• these organisms do not invade the bladder because the
urethra is periodically flushed by acidic urine.
INDIGENOUS MICROFLORA
OF HUMANS
• persistent, recurring UTIs often develop when there is an
obstruction or narrowing of the urethra, which allows the
invasive organisms to multiply.
• The most frequent causes of urethral infection :
Chlamydia trachomatis, Neisseria gonorrhoeae, and
mycoplasmas.
• introduced into the urethra by sexual intercourse.
• The reproductive systems of both men and women are usually
sterile, with the exception of the vagina.
• the microflora of the vagina varies with the stage of sexual
development.
INDIGENOUS MICROFLORA
OF HUMANS
• During puberty and after menopause, vaginal secretions are
alkaline
• supporting the growth of various diphtheroids, streptococci,
staphylococci, and coliforms (E. coli and closely related enteric
Gram-negative bacilli).
• Through the childbearing years, vaginal secretions are acidic
(pH 4.0–5.0).
• encouraging the growth mainly of lactobacilli, along with a
few α-hemolytic streptococci, staphylococci, diphtheroids,
and yeasts.
INDIGENOUS MICROFLORA
OF HUMANS
• Bacteria found in the vagina include species of Actinomyces,
Bacteroides, Corynebacterium, Klebsiella, Lactobacillus,
Mycoplasma, Proteus, Pseudomonas, Staphylococcus, and
Streptococcus.
• The metabolic byproducts of lactobacilli, especially lactic acid,
inhibit growth of the bacteria associated with bacterial
vaginosis (BV).
• Factors that lead to a decrease in the number of lactobacilli in
the vaginal microflora can lead to an overgrowth of other
bacteria.
INDIGENOUS MICROFLORA
OF HUMANS
• Bacteroides spp., Mobiluncus spp., Gardnerella vaginalis, and
anaerobic cocci, which in turn can lead to BV.
• a decrease in the number of lactobacilli can lead to an
overgrowth of yeasts, which in turn can lead to yeast vaginitis.
BENEFICIAL AND HARMFUL ROLES
OF INDIGENOUS MICROFLORA
BENEFICIAL AND HARMFUL ROLES
OF INDIGENOUS MICROFLORA
• Certain of our intestinal bacteria are beneficial to us in that
they produce useful vitamins and other nutrients.
• Microbial Antagonism
• microbes against microbes.
• indigenous microflora serve a beneficial role by preventing
other microbes from becoming established in or colonizing a
particular anatomic location.
• microbial antagonism involve the production of antibiotics
and bacteriocins.
• colicin, a bacteriocin produced by E. coli.
BENEFICIAL AND HARMFUL ROLES
OF INDIGENOUS MICROFLORA
• Opportunistic Pathogens
• Opportunistic pathogens (opportunists) can be thought of as
organisms that are hanging around, awaiting the opportunity
to cause infections.
• Huge numbers of E. coli live in our intestinal tract.
• When reach bloodstream ,urinary bladder and wound ,it can
cause infection.
• Other opportunistic pathogens: Staphylococcus aureus, and
Enterococcus spp.
BENEFICIAL AND HARMFUL ROLES
OF INDIGENOUS MICROFLORA
• Biotherapeutic Agents
• When the delicate balance among the various species in the
population of indigenous microflora is upset by antibiotics,
other types of chemotherapy, or changes in pH, many
complications may result.
• Certain microorganisms may flourish out of control, such as
C. albicans in the vagina, leading to yeast vaginitis.
• diarrhea and pseudomembranous colitis may occur as a
result of overgrowth of Clostridium difficile in the colon.
BENEFICIAL AND HARMFUL ROLES
OF INDIGENOUS MICROFLORA
• Cultures of Lactobacillus in yogurt or in medications may be
prescribed to reestablish and stabilize the microbial balance.
• Bacteria and yeasts used in this manner are called
biotherapeutic agents (or probiotics).
• Other microorganisms that have been used as biotherapeutic
agents include Bifidobacterium spp., nonpathogenic
Enterococcus spp., and Saccharomyces spp. (yeasts).
MICROBIAL COMMUNITIES
(BIOFILMS)
MICROBIAL COMMUNITIES
(BIOFILMS)
• A biofilm is any group of microorganisms in which cells stick
to each other on a surface.
• consists of a variety of different species of bacteria plus a
gooey extracellular matrix that the bacteria secrete
• extracellular matrix composed of polysaccharides, proteins,
and nucleic acids.
• The bacteria grow in tiny clusters—called microcolonies—that
are separated by a network of water channels.
• The fluid that flows through these channels bathes the
microcolonies with dissolved nutrients and carries away
waste products.
MICROBIAL COMMUNITIES
(BIOFILMS)
• Biofilms have medical significance
• They form on bones, heart valves, tissues, and inanimate
objects such as artificial heart valves, catheters, and
prosthetic implants.
• It has been estimated that perhaps as many as 60% of human
infections are due to biofilms.
• Biofilms have been implicated in diseases such as
endocarditis, cystic fibrosis, middle ear infections, kidney
stones, periodontal disease, and prostate infections.
MICROBIAL COMMUNITIES
(BIOFILMS)
• Dental plaque consists of a community of microorganisms
attached to various proteins and glycoproteins adsorbed onto
tooth surfaces.
• If the plaque is not removed, substances produced by these
organisms can penetrate the tooth enamel, leading to
cavities, and eventually causing soft tissue disease.
• Biofilms are very resistant to antibiotics, disinfectants, and
certain types of host defense mechanisms.
MICROBIAL BIOTECHNOLOGY
Definition
Production of therapeutic proteins.
Production of DNA vaccines
Production of vitamins
Use of microbial metabolites as antimicrobial
agents and other types of therapeutic agents.