1. Endogenous Microbial FloraBY
Prof. DR. Zainalabideen A. Abdulla,
DTM&H., MRCPI, Ph.D., FRCPath. (U.K.)

2. Learning Objectives

3. Microbial Ecology
Is the study of the numerous interrelationships between microbes and the world around them.
Example:
Microbes with human in causing diseases (bad guys); while others are beneficial in many aspects

4. Symbiosis/Symbiotic (mutualistic) relationship
Is the living together in close association between two different organisms (Symbionts):
• Beneficial to one or both
• Harmful to one
• Neutralism: Neither is affected

5. Commensalism Mutualism
Beneficial to one with no consequence on the other
e.g. Demodex (mite) and hair follicle
Mutualism
Beneficial to both symbionts
e.g. E. coli in intestine & vitamin K production

6. Parasitism Opportunistic
Beneficial to one (parasite) and detrimental (harmful) to the other (host)
e.g. Trypanosoma gambiense and sleeping sickness
Opportunistic
Change from mutualistic or commensalistic to parasitic (disease causing) relationship

8. 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

10. Microbiota of the skin - Bacteria and fungi - Anaerobes > aerobes
(deep layers, hair follicles, sweat, sebaceous
glands)
- Most common Staphylococcus epidermidis,
Corynebacterium, Propionibacterium

11. Factors affecting skin microbiota - Anatomical location
- Moisture
- pH
- Temperature
- Salinity
- Chemical wastes
* Most infections after burn, wound or surgery come from the skin microbiota

12. 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

13. 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)

14. Microbiota of the oral cavity
- Anaerobes survive (shelter)
- Numerous microbes
- Alpha-hemolytic Streptococcus: Most common
- Streptococcus mutans: Dental plaque

15. 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 ( species)

16. Colon microbiota . Aerotolerant/ obligate anaerobes opportunistic
• Actinomyces, Bacteroides,
Clostridium, Enterobacter,
Enterococcus, E.coli (most common),
Klebsiella, Lactobacillus, Proteus,
Staphylococcus, Streptococcus
• Fungi, protozoa, viruses

17. 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)

18. Human microbiom Project (HMP)
- Started 2008
- Humans differ
- Most diversity unexplained
- Microbes have X360 more genes
- Stay and return to state of equilibrium

19. 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)

20. Opportunistic pathogens
- Many of indigenous microbiota
- Example:
E.coli: In intestine No harm
Out side intestine Pathogenic

21. 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)

22. 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

23. Cont./…Biofilm • 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

25. Synergism (Synergistic Infections)
• Two or more microorganisms team up
• Polymicrobial or mixed that neither could
cause
Example: Trench disease (Vincent disease)
caused by mixed bacteria

27. 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)