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 in-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!
what are the usually sterile zones in the body? (7)
- Blood
- Spinal fluid
- Internal portion of urinary tract (bladder, kidney)
- Peritoneal cavity (gut cavity)
- Pleural cavity (lung cavity)
- Sinuses
- Interior region of other body tissues (bones, muscle, …)
