Endogenous Microbial Flora BY 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. Example: Microbes with human in causing diseases (bad guys); while others are beneficial in many aspects

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

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

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

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 glands) - 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 No harm Out side intestine Pathogenic

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

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

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

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)