1. Microbial ecology and biotechnology Dr. Mohammad Shakeeb,MD Specialist in clinical pathology/microbiology and immunology

2. 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.

3. 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.

4. SYMBIOTIC RELATIONSHIPS INVOLVING MICROORGANISMS

5. 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.

6. SYMBIOTIC RELATIONSHIPS INVOLVING MICROORGANISMS parasitic relationships : are harmful to one symbiont.  Neutralis m 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.

7. 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).

8. 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.

9. 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.

10. 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.

11. 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.

12. INDIGENOUS MICROFLORA OF HUMANS

13. 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

14. 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

15. 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

16. 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).

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

22. 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.

23. 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.

24. 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.

25. 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).

26. 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.

27. 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.

28. 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.

29. 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.

30. 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.

31. 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.

32. BENEFICIAL AND HARMFUL ROLES OF INDIGENOUS MICROFLORA

33. 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.

34. 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.

35. 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.

36. 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).

37. MICROBIAL COMMUNITIES (BIOFILMS)

38. 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.

40. 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.

41. 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.

42. 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.