chapter 15

Question 1

human microbiome

Answer 1

• Commensals (resident): microorganisms routinely found on the bodies of most healthy inidividuals. Commensals normally colonize the body without causing an infection
  
  • Skin: 10^12
  • Mouth:10^10
  • Gstrointestinal tract: upto 10^13
    Colon: 90% of gastrointestinal tract bacteria, anaerobic environment

** so in animals, vast majority of microorganisms are in gastrointestinal tract

Question 2

animals as microbial habitats

Answer 2

• Animals are continually exposed to a great variety of microorgansims from the environment, from contact with other individuals and from ingestion of food and water
  
  • The bodies of animals provide a warm, wet and potentially highly nutritious environment for bacteria that have evolved ways to colonize it. There is an evolutionary pressure to do so.
  • Temp., ph, nutrient supply, the immune system (genetic factor) and other factos influence the richness and the abundance of the microorganisms on an individual
    As the animal develops, various body surfaces become progressively colonized: the indiviual acquires its normal microbiome

Question 3

relationship between animals and microorganisms

Answer 3

• At first, most microorganisms may seem to be commensals. They take advantage of the host (nutrients, shelter) and they do not harm the host
  
  • But, commensals can also be beneficials:
    1. Provide host with vitamins and metabolic pathways (gut)
    2. Provide protection against new incoming microbial populations (occupy the territory)
    3. Teach the immune system
    Also parasitism: some commensals can become pathogenic under specific conditions (and commensals of one species may cause infectious diseases in another)

Question 4

harmful relationships with microorganisms

Answer 4

• PATHOGENS: microbial parasites that are able to cause infection
  
  • INFECTION situation in which a microorganism is established and growing in a host, causing damage
  • DISEASE: damage or injury to the host that impairs host function (infectious diseases, autoimmune diseases, cancer)
  • PATHOGENICITY: the ability of a parasite to inflict damage to the host
  • VIRULENCE: measure of pathogenecity
    OPPORTUNISTIC PATHOGEN: causes disease only in the absence of normal host resistance. The normal microbiome contains opportunistic pathogens

Question 5

cellulose composition

Answer 5

• Microfibril structure in plant cell wall: contain hemicellulose, paracrystalline cellulose and crystalline cellulose
  Cellulose molecule: glucose and cellobiose

Question 6

GI tract of herbivores

Answer 6

• Herbivores live on plant material rich in cellulose and other insoluble polysaccharides (lignin, hemicellulose, pectin)
  
  • Animals lack the enzyme (cellulase) that is required to degrade cellulose
  • Microorganisms present in the GI tract of herbivores are able to degrade cellulose and provide the host with nutrients (mutualism, symbiotic relationship)
  • 2 digestive strategies have evolved in herbivorous animals:
    1. FOREGUT fermentation: fermentation chamber precedes the acidic stomach (ex:ruminants, colobine monkeys,hoatzin)
    HINDGUT fermentation: uses cecum and/or large intestine as fermentation chambers (ex: cecal animals, some rodents, reptiles, primates)

Question 7

rumen of ruminant animals

Answer 7

• Food is chewed minimally, swallowed, and passes into the rumen (foregut fermentation chamber)
  
  • pH of the rumen is maintained by salive which contains sodium bicarbonate and sodium phosphate
  • Rumen:
    1. 39-40 degree
    2. pH=5-7
    3. Anaeroic environment
    Cow: 100-150L, sheep:6L

Question 8

rumen of ruminant animals (how is it fermented)

Answer 8

• Only small proportion of the rumen’s microorganisms produce cellulases
  
  • Fermentation in the rumen is mediated by cellulolytic microbes that hydrolyze cellulose to fee glucose and cellobiose, that are then available to all microorgansims fro growth
  • The sugars are then fermented, producing volatile FA (VFAs: acetic, propionic, butyric), CH4 and CO2
    FA pass through the rumen wall into the bloodstream and are utilized by the animal as its main energy source

Question 9

rumen microorganisms

Answer 9

• Ciliated protozoa, bacteria, archaea (300-400 species, SSU rRNA sequencing)
  
  • Contains 10^10-10^11 microbes/g of rumen content
    Ex: bacteriodetes, firmicutes, methanogens)

Question 10

methanogens

Answer 10

• Methanogens produce CH4. strict anaerobe
  
  • 4H2 + CO2= CH2 + H20 + energy
  • CH3COOH = CH4 + CO2 + energy
  • CH3COOH= acetate
  • Acetate used by methanogens is not available to the host. Up to 10% of the energy value of the feed can be lost as CH4
    A compund called Monensin inhibits methanogenesis and is routinely added to feed to reduce production of CH4

Question 11

rumens of ruminants animals (way of nutrients after digestion)

Answer 11

• After several hours of microbial digestion, small portions of the rumen contents are regurgitated, well chewed and then swallowed again. Smaller food particles are collected by the reticulum and moved to the omasum, where excess water is collected
  The material then goes in the stomach (abomasym) and from there, to the intestines. The mass of microbial cells are subjected to digestion and serves as a major source of AA and vitamins

Question 12

non-ruminant herbivores

Answer 12

• Fermentation takes place in the caecum, provides organic acids absorbed by the animal
  
  • The microbial mass that grows on cellulose and other polysaccharides are not digested, and they are excreted
  • Therefore, animals with hindgut fermentation chambers have a higher dietary requirement for AA and vitamins than ruminants do
    Rabbits and hares get around this problem by consuming the faecal pellets they produce (coprophagy)

Question 13

hawaiian bobtail squid

Answer 13

• A mutualistic symbiosis between the marine bacterium Aliivibrio fischeri and the Hawaiian bobtail squid is a model of how animal-bacterial symbioses are established
  
  • The 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
    Transmission of bacterial cells is horizontal

Question 14

termites

Answer 14

• Termites decompose cellulose and hemicellulose
  
  • Diverse community of anaerobes including cellulolytic anaerobes
    Anaerobic bacteria and cellulolytic protists

Question 15

normal microbiome

Answer 15

• Most microorganisms are commensals, few contribute to health (beneficial) and fewer pose direct threats to health (harmful)
  
  • Normal microbiome:
    1. Microorganisms usually found associated with human body tissue
    2. Humans are colonized by microorganisms at birth
    Normal microbiome changes over time and according to the condition of the host (diet, environment, aged, sex, occupation)

Question 16

normal microbiome of the skin

Answer 16

• The epidermis is composed of an inner layer of living, actively replicating cells and an outer layer of dead cells
• Sebaceous glands, apocrine sweat glands: secretes salt water, with various amouns of proteins, lipids, and sugars. Secretions are slightly acidic and have some antimicrobials effects (lipids an proteins)
  
  • Dead cell layer forms a tough barrier that prevents microorganisms from penetrating deeper tissues
  • The skin is generally a dry, acid environment that does not support the growth of most microorganisms
  • The ducts that carry secretions to the surface are colonized by only a few well-adapted species (Gram-positive)
  • The normal microbiome secretes bacteriocin that kills incoming competitors and protects- to a certain extent- against colonization by harmful bacteria
    The skin may also harbor anaerobes (aerotolerant): propionobacterium acnes inhabits hair canals

Question 17

name of the bacteria in the skin

Answer 17

• Yeasts, molds, bacteria
  
  • Ex: mycobacterium, staphylococcus, streptococcus
  • Gram positive: actinobacteria, firmicutes
  • Gram negative: bacteriodetes, proteobacteria
  • Sebaceous skin: majority is propionibacteria, staphylococci
  • Moist skin: corynebacteria, staphylococci
    Dry skin: betaproteobacteria, corynebacteria

Question 18

oral cavity

Answer 18

• The oral cavity is a complex, heterogenous microbial habitat. Both aerobic and anaerobic niches are available
  
  • High concentrations of nutrients near surfaces in the mouth promote localized microbial growth
    The teeth consist of a mineral matrices (enamel) surrunding living tissue (dentin and pulp)

Question 19

dental plaque

Answer 19

• Bacteria colonize tooth surfaces by first attaching to acidic glycoproteins deposited there by saliva
  
  • Extensive grwoth of oral microorgansims, especially streptococci, results in a thick bacterial layer (dental plaque). In the presence of sucrose-from diet- streptococcus mutans synthesizes extracellular polysaccharides (dextran) that aid its attachment to the tooth surface (form an extracellular matrix, ECM)
  • As plaque continues to develop, anaerobic bacterial species begins to grow
    The microorganisms in dental plaque (S. mutans and various lactobacilli) ferment sucrose and produce lactic acid that demineralizes the tooth enamel (solubilizes calcium)

Question 20

Gastrointestinal tract of humans- major physiological processes

Answer 20

1. Esophagus:
   
   • Secretion of acid (HCl)
   • Digestion of macromolecules
   • pH=2
     2. Small intestine:
   • Continued digestion
   • Absorption of monosaccharides, AA, FA, water
   • pH 4-5
     3. Large intestine:
   • Absorption of bile acids, vitamin B12
     pH= 7

Question 21

gastrointestinal tract of humans

Answer 21

• Colonization begins at birth. Microbial populations in different areas of the GI tract are influenced by diet and the physical conditions in the area
  The acidity of the stomach and the duodenum of the small intestine (pH=2) prevents many organisms from colonizing the GI tract. Microorganisms in food particles might be protected

Question 22

microorganisms in human colon

Answer 22

• Mostly strict anaerobes or facultatives aerobes: bacterioides (23%), enteric bacteria (E.coli), yeasts, anaerobic protozoa (entamoeba coli). High variability in gut communities between different individuals
  
  • Microorganisms digest complex carbohydrates (cellulose, starch..) and produce VFAs
  • Intestinal microorgansism of the large intestine ferment VFAs and produce gas (CO2 and H2). Methanogens convert CO2 and H2 to CH4 (found in 1/3 of adults)
  • Sulfate reducers and organisms that can ferment ceysteine and methionine produces H2S. Organosulfur compunds (methanethiol) are responsible for the smell
  • Intestinal microorganisms carry out a cariety of essential metabolic reactions that produces various nutrients that benefit the host: (AA, vitamine like B12,K,thiamine, riboflavin..)
  • Microorganisms contribute to the maturing of the gastrointestinal tract
  • Microbes in the gut affect early development, health, and predisposition to disease
    Gut microorgansism may play a role in obesity (low H2 promotes fermentation and creation of CH4)

Question 23

respiratory tract

Answer 23

• Microbiome of the nose and nasopharynx is very similar to that of the mouth: stalphylocicci, streptococci, corynebacteria
  
  • Nasopharynx may harbor potential pathogens that are under control by host immune systemsL streptococcus pneumonia, haemophilus influenzae, neisseria meningitidis. HEALTHY CARRIER
    The lower respiratory tract, including trachea, bronchi and lungs was historically considered free of microorganisms in healthy individuals (using the culture technique). Recent study shows that the lower respiratory tarct also harbors a microbiome (low biomass)

Question 24

genitourinanry tract

Answer 24

- Genitourinary tract of men and the urinary tract of woman are generally free of microorganisms due in part to the flushing action of urine
Altered conditions (such as change in ph) can cause potential pathogens in the urethra to multiply and cause disease. A few of the normal microorganisms of the gastrointestinal tract can cause urinary tract infections (e. coli, proteus mirabilis)

Question 25

vaginal tract

Answer 25

• Variety and types of organisms present depend on age of the individual
  
  • Hormones control the glycogen concentration of the vaginal epithelium
  • Microorgansism degrade glycoegn and produce lactic acid which reduces the ph of the vaginal tract
  • Before puberty and after menopause: glycogen=low, ph of vaginal secretion=alkaline, microbial flora= staphylococci, streptococci, coliforms, corynebacteria
    Sexually mature: glycogen=high, ph of vaginal secretion=acidic, microbial flora=lactobacilli, streptococci,corynebacteria,candida albicans

Question 26

sterile zone (normally)

Answer 26

• 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)