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Endogenous Microbial Flora
Prof. DR. Zainalabideen A. Abdulla,
DTM&H., MRCPI, Ph.D., FRCPath. (U.K.)
Learning Objectives
Microbial Ecology
Is the study of the numerous interrelationships
between microbes and the world around them.
Microbes with human in causing diseases (bad
guys); while others are beneficial in many
Symbiosis/Symbiotic (mutualistic)
Is the living together in close association
between two different organisms (Symbionts):
• Beneficial to one or both
• Harmful to one
• Neutralism: Neither is affected
Beneficial to one with no consequence on the
e.g. Demodex (mite) and hair follicle
Beneficial to both symbionts
e.g. E. coli in intestine & vitamin K production
Beneficial to one (parasite) and detrimental
(harmful) to the other (host)
e.g. Trypanosoma gambiense and sleeping
Change from mutualistic or commensalistic to
parasitic (disease causing) relationship
Indigenous Microbiota of Humans/Human
Microbiome/Human Bioneme
- Human cells: 10 Trillion
- Microbiota: 100 Trillion (of 10,000 species)
- Fetus has no indigenous microbiota
- Sterile: Blood, lymph, CSF, internal organs
- Resident, Transient
- Washed/flushed out, pH, antibiotic
- Candida near body openings, e.g. mouth
Microbiota of the skin
- Bacteria and fungi
- Anaerobes > aerobes
(deep layers, hair follicles, sweat, sebaceous
- Most common Staphylococcus epidermidis,
Corynebacterium, Propionibacterium
Factors affecting skin microbiota
- Anatomical location
- Moisture
- pH
- Temperature
- Salinity
- Chemical wastes
* Most infections after burn, wound or surgery
come from the skin microbiota
Microbiota of the Ears and Eyes
- Middle and inner ear: sterile
External ear: As the skin microbiota
- Eyes: Tears, lysozyme, mucous, sebum
all reduce microbiota
Microbiota of the Respiratory Tract
- Upper RT (Nasal passages + throat “pharynx”)
- Lower RT (larynx, trachea, bronchi,
bronchioles and lungs)
• Moist, warm mucous
• Healthy carriers, e.g. diphtheria, meningitis
• Lower RT: Free of microbes (defenses)
Microbiota of the oral cavity
- Anaerobes survive (shelter)
- Numerous microbes
- Alpha-hemolytic Streptococcus: Most common
- Streptococcus mutans: Dental plaque
Microbiota of the GIT
- Parts esophagus to anus + glands + Organs
- Stomach pH 1.5: Barrier
• Helicobacter pylori: can live
- Duodenum: Few microbes
- Jejunum and ileum: More microbes
- Colon: Largest numbers (500-600 species)
Colon microbiota
. Aerotolerant/ obligate anaerobes opportunistic
• Actinomyces, Bacteroides,
Clostridium, Enterobacter,
Enterococcus, E.coli (most common),
Klebsiella, Lactobacillus, Proteus,
Staphylococcus, Streptococcus
• Fungi, protozoa, viruses
Microbiota of the GU Tract
- Kidney, ureter, bladder: Sterile
- External opening: Bacteria, yeast, viruses
- Reproductive system: Sterile, except vagina:
• After menopause: pH alkaline
(G+ & G- bacteria)
• Childbearing: pH acidic
(Lactobacilli & others)
Human microbiom Project (HMP)
- Started 2008
- Humans differ
- Most diversity unexplained
- Microbes have X360 more genes
- Stay and return to state of equilibrium
Microbial antagonism
- Microbes vs (or against) Microbes
- Prevent others from colonization (compete
for space and nutrients)
- Secrete antibiotics and bacteriocins (proteins
that kill other bacteria, e.g. colicin of E. coli)
Opportunistic pathogens
- Many of indigenous microbiota
- Example:
E.coli: In intestine
Out side intestine
No harm
Biotherapeutic Agents (Probiotics)
- Imbalance in microbiota if occurs, e.g.:
. Vaginitis (C. albicans)
. Pseudomembranous colitis (C. difficile)
Probiotics ingested to reestablish balance
. Bacteria (Bifidobacterium)
. Yeasts (Saccharomyces)
. Yogurt/Activia (Lactobacillus)
Biofilm (microbial communities)
• Microbes organized into biofilms
• Are complex and persistent communities
Example: Dental plaque, slime over tubes
• Different species + Matrix
• Microcolonies + Channels for fluid/nutrients
• Medical importance, e.g. on catheters, valves
• Diseases (60%): e.g. Endocarditis
• Very resistant to antibiotics (penetration,
inactivation, slowly growing, etc.)
• Cooperation between members (nutrients, wastes)
• Frustrated phagocytosis (damage to surrounding
tissues) and suppressed
• Treatment now to attack biofilms
Synergism (Synergistic Infections)
• Two or more microorganisms team up
• Polymicrobial or mixed that neither could
Example: Trench disease (Vincent disease)
caused by mixed bacteria
Microbial Biotechnology
• Production of therapeutic proteins, e.g insulin
• Production of DNA vaccine
• Production of vitamins, e.g. B12, K2, B2
• Production of antimicrobial agents
• Agricultural applications
• Food technology
• Production of chemicals
• Bio-mining
• Bioremediation (clean up various wastes)
• Industrial (e.g Aspartame sweeter production)