EBIO 3400 1st EditionExam # 3 Study Guide Lectures: 19 - 26The Human MicrobiomeWhat does it mean when we say that we live in a microbial world?- Archaea and bacteria the biggest majority- Multicellular lineages such as the corn, humans and fungi (in eucarya) make up a tiny diversity of life so not diverse b/c don’t use sequencing technologies like we do in the other two kingdoms- Microbes that are difficult to cultivate are used by extracting DNA and amplify that marker and sequence it and get the bases of the DNA to examine them, this is measuredby extracting the SSU rRNA gene (or part of it) so most molecular diversity can be found in microbes since (99% or more) microbes cant be cultured so only known from sequences Since microbes are ubiquitous, how do they provide key ecosystem services?- Regulation the outbreaks of diseases, regulation of climate, carbon cycles, water quality, crop production - Loss of ecosystem processes will lose some diversity of microbial communities- Restoration: microbial species  Can occupy any area that has resources for the microbes to live What is some support that developed from early observations?- Animalcules in enormous amounts of water and billions observed in the mouth- E. coli is though as a gut microbe but only because its easy to grow in the lab- But now, if you count the total number of human cells and all the microbial cells that areassociated with our body, we are really a minority <10% of all the cells that we carry, belong to us, mostly bc our cells are so much bigger than microbe cells - We outsourced a lot of our functions to microbes, Microbes contribute a lot of genes to the human ecosystem, Less than 1% to what we really contribute - Around 20 thousand genes in human - Our evolutionary adaptations are outsourced to microbes who have shorter life cyclesHow do microbes make the human genome unique?- Any two random humans have 99.9% identical genomes but what make us unique are our microbial symbionts. Become unique when we compare the microbial genes in our bodies How are microbes distributed over our bodies? How do microbes change overtime? How do microbes affect our health?Define “normal microbiota” or in other words the human microbiome.- Live on or with humans, most are non-pathogenic, commensals or mutualists (derive benefit from the host but do not harm the host), vary with type of tissue/condition (can reach a disease state if on a certain spot in tissue), specialized to specific parts of body- Can cause disease if reach abnormal location or are thrown off “balance” (i.e. too much sugar consumption, antibiotic treatment, wrong diet and sacrifice their function that they provide for us)Slide 59 human microbiome What are the main reservoirs in the body for microbes?- mouth (10^10), GI tract (10^14) and skin (10^12)Give an example how the skin area is specific to certain microbes?- Not all microbes can function in certain areas of the skin where there is production of salt and sweat glands b/c it draws water away from microbes: subcutaneous, anti-microbial compounds like lysosomes that dissolve some microbes- Moisture loving microbes cant live in subcutaneous - Very selective for very specific microbes Why is the skin difficult to colonize and what kind of microbes inhabit the skin? What microbes inhabit moist areas?- Dry, salty, acidic, protective oils so hard to colonize - Most microbes in moist areas: Scalp, ears, armpits, genital and anal areas-Mostly Gram-positive bacteria More resistant to salt and dryness- Staphylococcus epidermidis (S. epidermidis)- Propionibacterium acnesWhat are some variables that regulate potential lifestyle of some microbes pertaining to the skin?- pH, moisture availability, temperature, UV exposure, O2/CO2Describe the skin pH in adults. Why is low pH a beneficial element?- Skin pH averages 5.5 (in adults), 7.0 (in children)- Acidity due to sebum (fatty acids and triglycerides) production and fermentation (to short fatty acids and priopionic acid) by Priopionibacterium acnes - The bacterium uses the products through a fermentative process and degrades them to short fatty acids and propionic acids (establishes a low pH of the skin)- Due to sebaceous glands that produce oil - Children have more neutral pH which is one of the reasons why kids get more skin infections more prominently than adults (protective 1st defense factor) - Leading cause of excess oil: through hormones, lifestyle, diet that throws off the bacterial community - Low pH also makes it an unfavorable environments to help ward off bas microbes defense shield - Excessive production of oils in adolescence leads to excessive production of fatty acids that may block the sebum channels. An increased bacterial abundance may trigger inflammation (immune system response process) What bacterium is used to make Swiss cheese and closely related to priopionibacterium acnes?- Propionibacterium freudenreichii List the area of the most cells on the skin surface to the least using these 5 terms: Forehead, forearm, back, armpitArmpit > forehead > back > forearm Slide 24 dominant bacteria taxa in skin How are washing hands beneficial to removing bacteria? - REMOVES: 90% of transient bacteria- 40% of resident bacteria- Presence of skin microbiome inhibits infection by Staphylococcus aureus- Brings microbes out of acidic environment and more neutral when we wash our hands - S. aureus: natural component of skin microbiome, translocated to another part of the body can make it become lethal Describe the microbial community in the mouth? What about in infants? - 1010 bacterial cells, 500 – 1000 bacterial ‘species’ per mouth- Human’s infant mouth is colonized with nonpathogenic: Dominant ones - Neisseria (G-negative cocci)- Streptococcus and Lactobacillus (G-positive rods)- As teeth emerge (anaerobic space), other bacteria grow- Prevotella and Fusabacterium: between gums and teeth- Streptococcus mutans: attached to tooth enamel- Organisms must survive: - Mechanical removal by adhering to gums and teeth- Chemistry of saliva (1 – 100 mL/hr) that contains lysozymes, lactoferrin, antimicrobial compoundsHow are Lactobacillus salivarius and Candida albicans related to each other?- Lactobacillus is a lactic acid fermenter and a controller for candida- Candida: fungus, takes advantage of absence of Lacto. SalivariusWhat exactly is dental plaque and what bacterium is the main cause of it?- Dental plaque: biofilm bacterial community