Microbial+Ecology+Fall+2024.pdf

Microbial Ecology NURS:201 Week 6 Department of Microbiology, Immunology and Pharmacology Makeda Matthew-Bernard [email protected] Lecture outline Introduction Symbiotic relationships Indigenous microflora of humans Microflora of the skin Microflora of the ears and eyes...

Microbial Ecology NURS:201 Week 6 Department of Microbiology, Immunology and Pharmacology Makeda Matthew-Bernard [email protected] Lecture outline Introduction Symbiotic relationships Indigenous microflora of humans Microflora of the skin Microflora of the ears and eyes Microflora of the respiratory tract Microflora of the oral cavity Microflora of the gastrointestinal tract Microflora of the genitourinary tract Beneficial and harmful roles of indigenous microflora Microbial communities (biofilms) Microbial biotechnology Learning objectives Discuss the four categories of symbiotic relationships Differentiate between mutualism and commensalism and give an example of each Explain dysbiosis and how it can impact the body Explain the variation in the microbiota with body site Discuss transient microbiota Differentiate between an endogenous and an exogenous infection Describe the beneficial and harmful roles of the indigenous microbiota Discuss how the microbiota changes and the factors that affect it Describe biofilms and their impact on human health Discuss the role of microorganisms in agriculture and biotechnology Introduction: What is microbial ecology? “The study of the relationships and interactions within microbial communities (e.g., environment-host-microbe) within a defined space” E.g., how our microorganisms help us stay healthy: Beneficial microorganisms in the gut and on the skin’s surface Microbial ecology looks at: How (types of relationships and effects) Who (the different species; numbers) Where (in and on the body) Symbiotic relationships involving microorganisms Symbiosis Two or more different biological species living together for a long period of time in close association https://x.com/FrontMicrobiol/status/856511296828657664 Symbiotic relationships involving microorganisms Neutralism is a symbiotic relationship in which neither symbiont is affected by the relationship Different microorganisms occupy the same ecologic niche but have absolutely no effect on each other Symbiotic relationships involving microorganisms Communalistic (Commensalism) One benefits; the other doesn’t benefit/isn’t helped, but also isn’t harmed This is mostly the normal microflora on our body Symbiotic relationships involving microorganisms Mutualistic (mutualism) Both benefit “a reciprocal arrangement” Microorganisms in our gut: E. coli in the large intestines synthesizes vitamin K and some B vitamins The protozoa that live in the intestine of termites produce enzymes that break down the wood into usable form Lichens that you see as colored patches on rocks and tree trunks also mutualistic relationship Symbiotic relationships involving microorganisms Parasitic (Parasitism) One organism benefits while the other is harmed or damaged Symbiotic relationships involving microorganisms Parasitic can mean: An infection due to a parasite (eukaryotic microorganism such as a hookworm) OR A harmful relationship Outcomes of parasitism: Infection without damage Nonpathogenic intestinal protozoa Smart parasite it takes the nutrients it need to survive from the host but does not cause disease Infection with harm/damage (i.e., disease) Virus infecting a host cell Host cell dies  Various symbiotic relationships Symbiotic A. Mutualistic: Algal cell and the fungi make Lichen B. Communalistic: The Dermodex mites that live in human hair relationships follicles C. Parasitic: The flagellated protozoan that causes African sleeping sickness (Trypanosoma gambiense)  Dysbiosis Dysbiosis- imbalance of the microbiome Changes in conditions can cause one type of symbiotic relationship to shift to another type Conditions can cause a mutualistic or communalistic relationship between humans and their indigenous micro biota to shift to a parasitic, disease- causing (pathogenic) relationship Dysbiosis makes us more vulnerable to infections from germs living inside and outside of our bodies https://ecosh.com/dysbiosis-microbial-imbalance-symptoms-causes-and-natural-treatment/ Indigenous Microflora of Humans Normal microflora or resident microflora Includes all the microbes (bacteria, fungi, protozoa and viruses) that reside on and within a person; sometimes referred to as our “normal flora” Blood, lymph, spinal fluid, and most internal tissues and organs are normally free of microorganisms (i.e., they are sterile). Destruction of resident microflora disturbs the delicate balance between host and microorganisms. https://www.whatisbiotechnology.org/index.php/science/summary/microbiome/the-human-microbiome-refers-to-the-complete-set-of-genes  Sterile sites- Microbe free Fluids within an organ or tissue E.g. blood, Internal organs Internal tissues cerebrospinal fluids , semen (before entering E.g. heart, liver, brain, kidney E.g. muscles, glands , bone urethra), urine in kidneys and bladder https://www.kidneyfund.org/all-about-kidneys/other-kidney-problems/hepatitis-c/hepatitis-c-and-liver https://www.smithsonianmag.com/science-nature/your-blood-type-lot-more-complicated-you-think-180951669/ Transient Microbes Transient microbiota take up temporary residence on and within humans Derived from the environment, does not typically cause disease, and does not establish itself permanently on the surface Members of the transient flora are generally of little significance if the normal resident microbes are intact If the resident microbes are disturbed, transient microbes may colonize, proliferate and cause disease https://www.brevis.com/blog/2016/05/transient-germs-facts/ Transient flora vs Resident flora Transient flora includes microbes that are temporarily harbored on or inside the body while resident flora are microbes that permanently reside in specific anatomical sites of the human body  Some infectious disease are due to normal flora ENDOgenous EXOgenous Acquired from within (host Acquired from an microbiome) outside/EXternal source Normal flora gets into: Contact with animals Bloodstream Contact with infected people Organs Insect bites Tissues Food Microflora gets out of Water Soil control Examples: Examples: Thrush (C. albicans) Cholera (contaminated water) Folliculitis (S. aureus) Covid (infected humans) Bacterial vaginosis (Lactobacillus) Rabies (infected animal) What else impacts the microorganisms present? Oral microflora changes as children develop milk Age teeth and then permanent teeth Transition from milk to solids Diet Meat eating versus vegetarian Pets, insects External environment Hot and humid versus dry climates Medical conditions (e.g., diabetes) and medications (e.g., antibiotics) Genetic General host defenses Physical barriers Skin Keratin Mucous membranes (e.g., throat, mouth) Trap, destroy pathogens Mucous layers sheds off Cilia remove microbe from lungs Chemical barriers to infection Acidic pH: stomach, skin, vagina Why is it important to understand who is where? Changes in the balance can make infection more likely Normal flora can cause disease under some circumstances: Protective microorganisms get unbalanced - harmful microorganisms take over and cause damage: Antibiotic associate diarrhea (bacterial infection due to Clostridium difficile) Vaginal and oral thrush (Candida infection) Opportunistic infections Microorganisms can get into protected sites or locations From throat to central nervous system - meningitis From skin surface into bloodstream and onto heart valves - endocarditis From mouth into lungs - pneumonia Resident microbiota can become pathogenic Opportunistic pathogens Can become pathogenic if you are immunocompromised Surface breach allows bacterial entry. Oral thrush typically caused by the A MRSA infection A necrotizing streptococcal infection after fungus Candida albicans subcutaneous injection of a recreational drug https://www.mayoclinic.org/diseases-conditions/staph-infections/symptoms-causes/syc-20356221 https://dermnetnz.org/topics/skin-infections-in-people-who-inject-recreational-drugs https://www.healthline.com/health/hiv/oral-thrush-hiv#what-is-oral-thrush Where does the microbiota come from? Initially, colonization begins at birth Differs between vaginal birth(Lactobacillus and Bacterioides) and C- section (Staphylococcus aureus) Differs if the baby was breastfed (Bifidobacterium (infantis) or formula-fed (mixed population of coliform, lactobacilli, enteric streptococci) Throughout time: Physiological state- depressed and anxious vs not Infection Medications Diet Lifestyle  Indigenous Microbiota A person indigenous microbiota includes all the microbes (bacteria, fungi, protozoa, and viruses) that reside on and within that person.  Main take home messages: Different microbes are found at different sites Some are common to multiple sites Others are more specific to certain locations 1.Find an example of a species common to all 6 of the sites listed 2.Find an example of a site that only has one major group of bacteria Do not memorize this table Microbiota of the Skin Body’s largest organ (2m2) Serves as a physical barrier from foreign organisms Primarily bacteria and fungi – about 30 different types; most common = Staphylococcus spp. Number and variety of microorganisms depend on: Amount of moisture present pH Temperature Salinity Presence of chemical wastes and other microbes https://www.technologynetworks.com/immunology/articles/the-skin-microbiome-356627  Microbiota of the Skin Microbial population varies by site: Sebaceous (oily) - face, chest, back Moist- bend of elbow, back of knee, groin Dry- volar forearm and palm Difficult to colonize: Dry Acidic Protective oils- secrete lipid-rich sebum, a hydrophobic coating that lubricates and provides an antibacterial shield to hair and skin. Disease involvement: Propionibacterium acnes: Fatty acid induces inflammation Inflamed sebaceous gland Cause acne https://archdermatology.com/why-treat-acne/ Microbiota of the Ears and Eyes The middle ear and inner ear are usually https://www.aao.org/eye-health/anatomy/microbiome-of-eye sterile https://houstonsinusallergy.com/8-interesting-facts-about-human-ears/ Outer ear and the auditory canal contain the same types of microbes as are found on the skin Coughing, sneezing or blowing nose can move microorganisms into middle ear The external surface of the eye is lubricated, cleansed, and protected by tears, mucus, and sebum Microbiota of the respiratory tract Divided into: Upper Lower Lots of different microorganisms in various locations https://www.brainkart.com/article/Anatomy-of-the-Respiratory-System_21909/  Microflora of the Respiratory Tract Upper respiratory tract (nasal passages and throat) has an abundance of microorganisms; many are harmless, some are opportunistic pathogens Carriers harbor virulent pathogens in their nasal passages or throats, but do not have the diseases usually caused by these pathogens Examples: people harboring the bacteria that cause diphtheria (Corynebacterium diphtheriae), meningitis (Neisseria meningitidis) , whooping cough (Bordetella pertussis), and pneumococcal disease (Streptococcus pneumoniae) Lower respiratory tract is usually free of microbes https://www.brainkart.com/article/Anatomy-of-the-Respiratory-System_21909/  Microbiota of the Oral Cavity (Mouth) A shelter for numerous anaerobic and aerobic bacteria; remaining food particles provide a rich nutrient medium for bacteria Careless dental hygiene may cause: Dental caries (tooth decay) Gingivitis (gum disease) Periodontitis The most common organisms within the indigenous microflora of the mouth are various species of alpha- hemolytic streptococci https://www.mdpi.com/2075-4426/14/4/386  Plaque formation/Biofilm Dental caries A mixed infection of the tooth surface that gradually destroys the enamel May lead to destruction of the deeper tissue Major contributor: Streptococcus mutans Form sticky dextran slime layers in the presence of simple sugars The adherence of dextran to the tooth surface establishes the basis for a biofilm that attracts other bacteria https://www.winningsmiletor.com/dental-caries/  Microbiota of the gastrointestinal tract (GI) GI starts in the oral cavity The stomach is highly acidic and also contains gastric enzymes which usually prevents the growth of indigenous micro biota Most of the transient microbes that are consumed with our diet are killed as they pass through the stomach Helicobacter pylori - lives in stomach of some persons and is a common cause of ulcers Bile also inhibits microbial growth in upper part of small intestine The colon (large intestine) contains the largest number and variety of microorganisms of any colonized area of the body; an estimated different species - primarily bacteria Colon is anaerobic; bacteria in colon are mostly obligate-, aerotolerant-, and facultative anaerobes Many of the microflora of the colon are opportunists https://www.nursingtimes.net/clinical-archive/gastroenterology/gastrointestinal-tract-6-the-effects-of-gut-microbiota-on-human-health-21-10-2019/ Factors impact gut microbiota Helicobacter pylori Helicobacter pylori (H. pylori) bacterium has a role in gastritis and peptic ulcer disease Marshall was unsuccessful in developing an animal model, so he decided to experiment upon himself He did a baseline endoscopy which showed normal gastric mucosa He drank a culture of the H. pylori and observed the changes over 14 days which reviled ulcers He treated himself with antibiotic He recovered promptly and thus had fulfilled Koch’s postulates for the role of H. pylori in gastritis Microbiota of the Genitourinary (GU) Tract The GU tract consists of the kidneys, ureters, urinary bladder, urethra, and parts of the female/male reproductive systems Kidney, ureters and urinary bladder are usually sterile; the distal urethra and its external opening harbor many microbes including bacteria, yeasts and viruses Most frequent causes of urethral infections include Chlamydia trachomatis, Neisseria gonorrhoeae, and mycoplasmas The male and female reproductive systems are usually sterile except the vagina https://liveutifree.com/what-causes-a-urinary-tract-infection/ Positive Effects of the Interactions between the Host and Its Microbiome Provides metabolic potential and supplies many vitamins and other nutritional factors Helps to train the immune system and supports host defense functions Affects neurodevelopment Has anti-Inflammatory properties Has antioxidant activity Resists colonization by pathogenic microorganisms Maintains a healthy digestive system Beneficial and Harmful Roles of Indigenous Microbiota Humans derive many benefits from their indigenous microflora; examples E.coli - vitamins K and B12. Microbial Antagonism Means “microbes versus microbes” Many members of our indigenous microflora are beneficial in that they prevent other microbes from becoming established Other examples of microbial antagonism involve: Production of antibiotics and bacteriocins (antibacterial proteins); an example is colicin, produced by E. coli Nutrient blocking: diverse gut bacteria consume the nutrients that a pathogen needs to grow, and this blocks the pathogen from invading the microbiome https://phys.org/news/2023-12-diverse-gut-bacteria-communities-pathogens.html  Producing harmful enzymes Replicating in and damaging cells and Harmful effects tissue are due to the Taking nutrients and resources microorganism Suppressing or triggering the immune system Producing toxic substances (toxins) Opportunistic Pathogens and Biotherapeutic Agents Opportunistic pathogens are those microorganisms that “hang around,” waiting for the opportunity to cause infection Examples: E. coli, other members of the family Enterobacteriaceae, S. aureus, and Enterococcus spp. The delicate balance of the indigenous microflora can be upset by antibiotics, other types of chemotherapy, and changes in pH Bacteria and yeasts used to stabilize the microbial balance are called biotherapeutic agents or probiotics Biotherapeutic Agents (probiotics) They are living (viable) microorganisms that are ingested to stabilize the microbial balance Can be taken in pill from which contain concentrated freeze-dried microorganism Bacteria Yeast Biotherapeutic Agents (probiotics) You can also get probiotics in less concentrated quantities from fermented foods and drinks, including: Yogurt and kefir Cottage cheese Miso soup Kombucha Sauerkraut or kimchi Pickles and pickle juice https://www.livofy.com/health/keto-diet/keto-friendly-probiotic-foods/  Microbial Communities It is rare to find an ecologic niche in which only one type of microorganism is causing a particular effect Microorganisms are often organized into biofilms – complex communities of assorted organisms Biofilms are everywhere; example – dental plaque Biofilms consist of a variety of different species of bacteria plus a gooey polysaccharide that the bacteria secrete; the bacteria grow in tiny clusters called microcolonies, separated by water channels Biofilms have medical significance; they form on urinary catheters and medical equipment and can cause diseases like endocarditis  Microbial Communities Microbes commonly associated with biofilms on medical devices include the yeast, Candida albicans, and bacteria like Staphylococcus aureus, Enterococcus spp., Klebsiella pneumoniae, and Pseudomonas aeruginosa. Biofilms are very resistant to antibiotics and disinfectants Antibiotics that are effective against pure cultures of organisms have been found to be ineffective against those same organisms within an actual biofilm Bacteria in biofilms produce different types of proteins that may not be produced by the bacteria in pure culture. Synergism Where an infection is due to two or more microorganisms “teaming up” Combination is greater than sum of the individual aspects Polymicrobial infections are usually due to a synergistic interaction: Polymicrobial – 2 or more causal agents (might be multiple bacterial species, bacteria and fungi, etc) Example: bacterial vaginosis, acute necrotizing ulcerative gingivitis (trench mouth) https://www.emdocs.net/em3am-acute-necrotizing-ulcerative-gingivitis/ Why aren’t we sick all the time? Not all microorganisms can cause disease Our immune defenses can keep lots of Physical barriers: intact skin, enzymes in sweat microorganisms under control Chemical barriers: acidity of the stomach Immune system can quickly recognize and respond to microorganisms that it has seen before The damage caused might be small and fixed quickly (depends on site and tissue affected) Role of our normal microflora in microbial antagonism Agricultural Microbiology There are many uses for microorganisms in agriculture Role of Microbes in Elemental Cycles Microorganisms play an important role in the cycling of nutrients and elements like nitrogen, carbon, oxygen, sulfur, and phosphorus. N2 is converted by nitrogen-fixing bacteria and cyanobacteria into ammonia (NH3) and ammonium ion (NH4).  Agricultural Microbiology There are a multitude of other microorganisms in soil – bacteria, fungi, algae, protozoa, viruses, and viroids; many are decomposers A variety of human pathogens live in soil including Clostridium spp. C. tetani – tetanus C. botulinum – botulism, use for Botox Bacillus anthracis- anthrax https://microbewiki.kenyon.edu/index.php/Clostridium https://textbookofbacteriology.net/Anthrax.html Biotechnology Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use Microbes are used in a variety of industries, including the production of certain foods and beverages, food additives, vaccines, and antibiotics. Many antibiotics and drugs are produced in pharmaceutical companies by fungi and bacteria (penicillin for example). https://microbenotes.com/penicillium-chrysogenum/ https://microbe-safari.org.uk/food-production/