7. Microbiology - Animals Flashcards
human microbiome: ___________ relationship –> explain!
- where do we have microbes + how many ish? (3 main)
COMMENSAL relationship! (resident)
- microorganisms routinely found on the bodies of most healthy individuals. Commensals normally colonize the body
without causing an infection –> they benefit from us + not clear what we gain from them!
- skin: 10^12
- mouth: 10^10
- gastrointestinal tract: up to 10^13 (1 kg) –> 90% of GI bacteria in the colon, anaerobic enviroment
ANIMALS as MICROBIAL HABITATS:
- animals are continually exposed to a great variety of microorgs from what? (3 ish)
- bodies of animals provide _____, ______ and potentially highly __________ environment fo bacteria that have evolved ways to colonize –> __________ pressure to do so
- what are the factors that influence the richness and abundance of microorgs on an individual? (5)
- as the animal develops, various body surfaces become progressively colonized: the individual acquires its normal ____________
- from environment: contact with other individuals and from ingestion of food and water + touch surfaces
- warm, wet and potentially highly nutritious (+ humans are a pretty stable environment) –> evolutionary pressure to do so
- temp, pH, nutrient supply, immune system (genetic factor) and other factors
- normal microbiome
relationship btw animals and micoorganisms
- define commensal relationship: good or bad for humans?
- commensals can also be __________ (3)
- can also have what relationship?
- COMMENSAL: take advantage of host (nutrients, shelter) –> they do not harm the host (we shelter them but more and more:
can be beneficial!:
- provide host with vitamins and metabolic pathways (gut)
- provide protection against new incoming microbial populations (occupy
the territory) –> microbes on your skin compete against invaders
- Teach the immune system (about what is a good/bad microbe)
PARASITISM: some commensals can become pathogenic under specific conditions (ie if conditions change/immune system becomes bad) –> and commensals of one species may cause infectious diseases in another
- in animals, vast majority of microrgs are found where?
- what are the 3 diets animals can have?
- phylogenetic studies suggest that dif lineages evolved a ___________ lifestyle
- does the phylogenetic tree of animals explain which diet animals have?
- in GI tract!
HERBIVORES: consume mostly plants
CARNIVORES: consume mostly meat
OMNIVORES: consume both plants and meat - evolved a herbivorous lifestyle
- no! random (just like how phylogenetic tree of bacteria doesn’t match with metabolic properties)
GI tract of herbivores:
- herbivores live on plant material rich in (2)
- what’s the problem? solution?
- what are the 2 digestive strategies that have evolved in herbivorous animals?
- in cellulose (polymers of glucose) and other insoluble polysacs (lignin, hemicellulose, pectin)
- animals need cellulase enzyme to digest cellulose
BUT no animals have cellulase - microrgs present in the GI tract of herbivores are able to degrade cellulose and provides host with nutrients (mutualism, symbiotic relationship)
- foregut fermentation: fermentation chamber (grows microbes and digest cellulose) precedes the acidic stomach
- hindgut fermentation: uses cecum and/or large intestine (after stomach) as fermentation chambers
which type of animals do foregut fermentation? explain the steps
RUMINANTS! like cows. moo
- eat grass –> food is chewed minimally, swallowed and passes into rumen (foregut fermentation chamber)
- after several hours of microbial digestion, small portions of rumen contents are regurgitated, well chewed and swallowed again
- smaller food particles are collected by reticulum and moved to omasum, where excess water is collected
- material then goes into stomach (abomasum) and from there, to intestines
- mass of microbial cells are subjected to digestion and serves as major source of aa and vitamins
- how big is the cow rumen? vs sheep?
- temperature?
- pH
- anaerobic or aerobic environment?
- how is pH of rumen maintained?
- cow: 100-150L
- sheep: 6L
- 39-40°C
- pH 5-7
- anaerobic (mostly fermentation + anaerobic met)
- pH of the rumen is maintained by saliva which contains sodium bicarbonate and sodium phosphate (buffers!)
describe the 3 (3rd one has 2 sub) trophic/food chain levels of the rumen of ruminant animals
- POLYMER DEGRADATION: cellulose and hemicellulose degraded to glucose
- SOLUBLE SUGAR UTILIZATION AND FERMENTATION
- glucose fermented by microorgs into lactate, succinate, propionate… –> volatile FA –> absorbed through rumen wall into cow bloodstream = main E source
3a. SECONDARY PRODUCT FERMENTATION
- volatile FA (lactate, succinate) –> butyrate, propionate (other volatile FA)
3b. METHANOGENESIS and ACETOGENESIS
- methanol + CO2 + H2 –> methane!!
- do all rumen microorg produce cellulase?
- fermentation in rumen is mediated by ___________ microbes that hydrolyse cellulose into ___A_____, that are available to all microorgs for _________
- _____A_____ are then ________ –> producing WHAT (3)
- rumen contains how many microbes/g of rumen content
- what types of microorgs? (3) + how many species?
- only a small proportion!
- cellulolytic microbes that hydrolyse cellulose into FREE SOLUBLE SUGARS (ie glucose) –> for growth!
- sugars are fermented, producing volatile FA (acetate, propionate, butyrate), CO2 and H2
- 10^10 - 10^11 microbes/g of rumen content –> very rich, diverse –> rich ecology
- ciliated protozoa, bacteria, archaea (300-400 species)
what is an important bacteria to know in the rumen of ruminant animals?
- contains 3 special structures ish
- RUMINOCOCCUS FLAVEFACIENS! main one that does cellulose degradation + use soluble glucose to produce volatile FA
- enzymes/cellulases
- scaffoldin
- cellulosome (on surface of ruminococcus: contains enzymes and scaffoldin (?) to help degrade cellulose)
- why do cows produce methane? how?
- metabolism?
- 2 bad consequences
- solution?
cows have methanogens! produce CH4 using H2 & CO2 OR acetate (CH3COOH)
- strict ANAEROBE
- up to 10% of energy value of the feed can be lost as CH4 (bc acetate used by methanogens is not available to the host) –> makes it more expansive to feed your cow)
- CH4 = bad for climate change
- monensin! antibiotic that inhibits methanogenesis and is routinely added to feed to reduce production of CH4
what is another name for in-gut fermenters?
- examples of animals
- fermentation takes place where?
- microbial mass that grows on (2) are digested/not digested and what happens to it?
- these animals have higher/lower dietary requirements for (2) than ruminants
- what is coprophagy?
- non-ruminant herbivores
- horse, rabbit, human
- takes place in caecum –> provides organic acids absorbed by the animal
- grows on cellulose and other polysacs are NOT digested –> are excreted
- HIGHER recs for aa and vitamins
- rabbits and hares get around this problem by consuming the faecal pellets they produce = COPROPHAGY
what animal + what bacterium is a model of how mutualistic animal-bacterial symbioses are established?
- explain their relationship! (2)
- transmission of bacterial cells is _____________
- marine bacterium Aliivibrio fischeri and the Hawaiian bobtail squid
- squid harbors large populations of the bioluminescent A. fischeri in a specialized structure (light organ)
- Bacteria emit light that resembles moonlight penetrating marine waters,
which camouflages the squid from predators (benefit for squid) vs squid provides nutrients for microbes - Transmission of bacterial cells is horizontal.
- are termites fore-gut fermenters or hind-gut fermenters?
- microbes in the termites’ gut decompose (2)
- termites have a diverse community of aerobes/anaerobes including WHAT (2 ish)
- hind-gut fermenters
- cellulose and hemicellulose
- anaerobes including cellulolytic anaerobes (rumnicoccus!!!) + anaerobic bacteria and cellulolytic protists
*are like mini-cows bc ruminococcus in their hindgut can digest cellulose + form short chain FA that are absorbed through the in-gut wall
NORMAL MICROBIOME IN HUMANS
- what relationship?
- microorgs are usually found associated with what?
- when are humans colonized by microorgs?
- does normal microbiome change over time? depending on what?
- commensal! some contribute to health (beneficial) and fewer pose direct threats to health (harmful pathogens)
- associated with human body tissue/anything that is exposed to outside
- colonized by microorgs at birth
- changes over time! according to condition of host (diet, environment, age, sex, occupation, etc.)
what happens to microbial richness and stability as you age from infancy to late senior?
- what can make a big change in your microbial diversity?
- richness starts low and increases as you get older and get exposed to different environments (daycare, illnesses, sexual activity, travel, pregnancy, relocation, etc.)
- stability: starts very low bc microbiota is not adapted to you body –> as you grow older: microbiome becomes more stable against changes (diet, infection, antibiotics) until retirement/late senior where it decreases bc of disease/meds, menopause…
- antibiotics! especially when you’re young/baby
NORMAL MICROBIOME OF SKIN
- epidermis is composed of which 2 layers + explain
- sweat glands secrete what (4) + are basic/acidic and some have what effects
- does dif parts of skin on your body harbour the same bacteria?
1) an inner layer of living, actively replicating cells
2) outer layer of dead cells –> forms tough barrier that prevents microorgs from penetrating deeper tissues
- salt water with various amounts of proteins, lipids and sugars
- slightly acidic + some antimicrobial effects (lipids and proteins)
- no! different parts contain different types of yeasts, molds, bacteria –> mycobacterium, staphylococcus, streptococcus
skin is generally a _____, ______ environment –> supports growth of most microorgs?
- what can be colonized by a few well-adapted species (gram-positive)
- normal microbiome secretes ________ that kills WHAT –> effect?
- skin harbours bacteria which what type of metabolism?
- dry and acid environment (+ a bit cooler: 33-34°C)–> does NOT support growth of most org
- ducts that carry secretions to the surface
- secretes bacteriocin that kills incoming competitors and protects (to a certain extent) against colonization by harmful bacteria
- mostly facultative or strict aerobes bc you have O2 BUT may also harbor anaerobes (aerotolerant): propionobacterium acnes inhabits hair canals
ORAL CAVITY MICROBIOME
- oral cavity is a complex, __________ microbial habitat
- aerobic or anaerobic?
- WHAT promotes localized microbial growth
- what makes it super complex?
- complex heterogenous microbial habitat
- both aerobic and anaerobic niches are available!
- high concentrations of nutrients near surfaces in mouth promote localized microbial growth
- bc has teeth! teeth = mineral matrices (enamel) surrounding living tissue (dentin and pulp) + crevasses (anaerobic zones)
DENTAL PLAQUE:
- how does bacteria colonize tooth surfaces?
- extensive growth of which microorg results in thick bacterial layer (also called what?)
- in presence of _________ , which bacteria syntehsizes WHAT that aid in WHAT
- as plaque continues to develop, which type of species start to grow?
- what causes tooth decay?
- by first attaching to acidic glycoproteins deposited there by saliva
- especially streptococci, results in thick bacterial layer (dental plaque)
- in presence of sucrose (from diet): streptococcus mutans synthesizes extracellular polysaccharides (dextran) that aid its attachment of the tooth surface (form an extracellular matrix)
- anaerobic bacterial species begin to grow (below surface)
- microorganisms in dental plaque – S. mutans and various lactobacilli –
ferment sucrose and produce lactic acid that demineralizes the tooth enamel (solubilizes calcium) = decay
GI tract of humans:
- colonization by microorgs begins when?
- microbial populations in dif areas of GI tract are influenced by (2)
- what is special about stomach and duodenum? –> consequence?
- mostly bacteria with what metabolism in GI tract? examples
- why high variability in gut communities btw dif individuals?
– begins at birth!
- diet + physical conditions in area (ie acidic stomach, enzymes, bile salts…)
- ACIDIC! (pH 2) –> prevents many organisms from colonizing the GI tract –> microorgs in food particles might be protected
- mostly strict anaerobes or facultative aerobes: Bacterioides, enteric bacteria (E. coli), yeasts, anaerobic protozoa (Entamoeba coli).
*we also have ruminococcus in our gut!
- bc we eat different things!
MICROORGANISMS IN HUMAN COLON
- microorgs digest WHAT and produce ___A______ –> _____A______ is absorbed in the colon
- then, who ferments ___A_____ and produce _____B_______ (2)
- then who converts ___B_____ into ____C______
- WHAT and organisms that can ferment cysteine and methionine —> produce ____D_____
- what are responsible for the bad smel?
- intestinal microorgs carry out a variety of essential _________ reactions that produce various nutrients (2) that benefit the host
- microorgs contrr=ibute to the (2)
- digest complex carbs (cellulose, starch) and produce volatile fatty acids (VFAs) –> absorbed in colon
- then intestinal microorgs of large intestine ferment VFAs and produce gas (CO2 and H2)
- methanogens convert CO2 and H2 into methane!
*some people have really high amounts of methanogen –> use up all the CO2 and H2 to make CH4, so bacteria continue producing lots of VFAs = more energy for human to adopt –> maybe cause of obesity - SULFATE REDUCERS and organisms that can ferment cysteine and methionine –> produce H2S in an anoxic environment
- H2S interacts with other organic material to form organosulfur compounds (ie methanethiol) –> responsible for smell
- metabolic rxns –> amino acids + vitamins (B12, K, thiamine, riboflavin, etc.)
- “maturing” of GI tract + training the immune system (teach what is a good vs bad bacteria)
- which part of the respiratory tract is sterile vs had bacteria?
- what kind of bacteria are found where?
UPPER respiratory tract: nasopharynx, nose, mouth, larynx, trachea –> harbor microorgs!
- microbiome of nose and nasopharynx is similar to that of mouth: staphylococci, streptococci, corynebacteria
- nasopharynx may harbour potential pathogens that are under contorl by host immune system: Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis
Healthy carrier: carry pathogen but doesn’t give damage –> can give to other people though
LOWER respiratory tract:
- trachea, bronchi and lungs –> mostly free of microorganisms in healthy individuals (using the culture technique). –> close to being sterile
*trachea filters to trap microbes + immune cells in alveolar sacs
- Recent study shows that the lower respiratory tract also harbors a microbiome (low biomass)
- are genitourinary tract of males and females generally free of microorganisms? why or why not?
- altered conditions (such as what) can cause potential pathogens in _________ to multiply and cause disease
- a few of the normal microorgs in WHERE can cause infections WHERE (2 ex)
- what is special about the vaginal tract to protect it against infection?
- yes! (despite urine being very nutritious) –> due in part to the flushing action of urine!
- such as change in pH –> in urethra (longer in males so harder for microorgs to climb up)
- from GI tract can cause infection in urinary tract (E. coli, proteus mirabilis)
- microorgs degrade glycogen and produce lactic acid which reduces pH of vaginal tract! vaginal tract has own microorgs that lowers pH!
