L14

Question 1

What is a microbiome?

Answer 1

The diverse community of organisms, including bacteria, viruses, fungi, and other microbes, that inhabit a particular environment, such as the human body, plant roots, or seawater.

Question 2

What is a holobiont?

Answer 2

A host organism and its associated community of symbiotic microorganisms, collectively functioning as a single ecological unit.

Question 3

Do humans provide a great habitat for microbes?

Answer 3

Yes, for microbes we are just like any other environment

Question 4

What is mutualism?

Answer 4

Where both partners gain

Question 5

Is the stability of the human microbiota critical to health?

Answer 5

Yes, diversity and abundance of the microbiome varies with host but also part of the body

Question 6

What varies between different locations in the GI tract?

Answer 6

Microbiota composition

Question 7

Why is the small intestine a harsh environment?

Answer 7

Short transit time, excretion of digestive enzymes and bile.

Question 8

What are the conditions in the colon?

Answer 8

Anaerobic, it is enriched with firmicutes and bacteroidetes, methanogens archaea present.

Question 9

In what way does microbial diversity in the gut vary?

Answer 9

Colon harbours trillions of bacteria, in exchange bacteria digest complex carbohydrates, boost immune system and fend off pathogens. Oral antibiotics can kill gut microbiome, reducing diversity and functionality.

Question 10

What types of bacteria are associated with human gut?

Answer 10

Strict anaerobes or facultative aerobes

Question 11

How is the gut microbiome assembled?

Answer 11

In a stepwise manner, newborns acquire some gut bacteria from their mothers. Quickly displaced and or outnumbered with the infants own bacteria. Increases in richness of bacteria as infants move from milk-based diet to an adult diet.

Question 12

How do bacteria assemble the gut microbiome?

Answer 12

Firmicutes are the first to colonise, proteobacteria are detected soon after followed by actinobacteria. Once food is introduced, bacteriodetes establish and displace most of the bacteria from other groups expect for the firmicutes.

Question 13

By what age is a child’s gut microbiome essentially adult like?

Answer 13

By school age, it is dominated by firmicutes and bacteriodetes

Question 14

As a host ages what increases?

Answer 14

Diversity and stability

Question 15

What is the difference in gut communities of individuals with obesity, insulin resistance?

Answer 15

Less diverse

Question 16

What is alteration in the gut microbiome called?

Answer 16

Dysbiosis

Question 17

As our association with the gut microbiota is mutualistic, what do bacteria get from us?

Answer 17

Gut environment is so good that it does not need to make amino acids, no need for sporulation in firmicutes

Question 18

As our association with the gut microbiota is mutualistic, what do we get from bacteria?

Answer 18

Firmicutes and bacteriodetes breakdown and ferment complex carbohydrates, and generate formate and short chain fatty acids (SCFAs).

Question 19

What do firmicutes produce?

Answer 19

SCFA butyrate which is absorbed by the colonic epithelium.

Question 20

What do bacteriodetes produce?

Answer 20

SCFAs acetate and propionate, distributed by the bloodstream to peripheral organs

Question 21

How is formate broken into CO2 and H2?

Answer 21

Methanogenic archaea remove hydrogen produced by fermentation carried out by firmicutes and bacteriodetes. Methanogenic archaea use CO2 as last electron acceptor and produce methane as byproduct. CO2 + 4H2 -> CH4 + 2H20

Question 22

What other bacteria are in the human gut?

Answer 22

Low abundant bacterial phyla - proteobacteria, actinobacteria, verrucomicrobia. Some commensal bacteria, some bacteria opportunistic pathogens. SCFAs if not absorbed by colonic epithelium help drop the pH of intestinal lumen to control growth of harmful bacteria

Question 23

Summary of SCFAs (butyrate, acetate, propionate)

Answer 23

Promote colonic health, consumed by other microbes, promote general health.

Question 24

What is fecal matter transplant?

Answer 24

Used to treat a severe bacterial infection, stool from healthy individuals used to restore gut microbiome

Question 25

What is the rumen microbiome?

Answer 25

SCFAs are also consumed by other microbes in the gut.

Question 26

What is syntropy and an example?

Answer 26

Interaction where one species feeds off metabolic products of another. E.g. what occurs in gut of ruminants

Question 27

Where does digestion of plant materials take place? And what environment is it?

Answer 27

Takes place in the rumen, which is an anaerobic environment. Bacteria, fungi, protozoa degrade cellulose and other plant-polymers into sugars, sugars are fermented into fatty acids.

Question 28

How do bacteria and fungi cooperate in the rumen?

Answer 28

By degrading and fermenting the plant-derived polymers to generate essential nutrients for the host.

Question 29

What are protists in the rumen involved in?

Answer 29

Cellulose degradation and predate on bacteria.

Question 30

What do archaea produce?

Answer 30

Methane from hydrogen and CO2.

Question 31

What increases fermentation rate?

Answer 31

Syntropic removal of H2, more ATP for microbes are produced

Question 32

What is commensalism?

Answer 32

One partner benefits, while the other is unaffected.

Question 33

What can commensal benefits include?

Answer 33

Amino acids, benefits, vitamins, and growth. Often host released products are waste products that the commensal organism scavenge.

Question 34

What do Bacteria do in our mouth? Steps 1-2

Answer 34

Bacteria colonise teeth and build multispecies-biofilms on the enamel dental plaque, first colonisers are streptococci and actinomycetes. Commensal bacteria form a biofilm that feeds on food debris that stick to it and establish mutualistic interactions and feed one another.

Question 35

What do Bacteria do in our mouth? Steps 3 - 5

Answer 35

If biofilm is left to grow pathogenic bacteria join the biofilm, pathogens grow leading to cavity formation and gum inflammation. S. Mutans ferments sugar and secretes acids. Excessive sugar allows S. mutans to produce more acid eroding enamel causing cavities. P. gingivalis can invade the gum epithelium inflammation and gum disease.

Question 36

What is parasitism?

Answer 36

Pathogenic bacteria that cause infectious diseases, pathogenic bacteria gain while host looses.

Question 37

What three challenges does an infectious agent confront?

Answer 37

Encounter, entry, establishment

Question 38

What happens in the encounter stage?

Answer 38

The host and infecting agent must meet. The source of the infecting agent may be the environment.

Question 39

What happens in the entry stage?

Answer 39

This can occur with or without penetration

Question 40

What is the establishment phase?

Answer 40

Overcoming the hosts defences, outcome of interactions between host and pathogen determines whether there will be symptoms of disease.

Question 41

What factors does establishment of disease depend on?

Answer 41

Inoculum size, virulence, host defences

Question 42

What are bacterial toxins?

Answer 42

Microbes that can cause disease by secretin toxins

Question 43

What can GI diseases be caused by?

Answer 43

Microbes secreting toxins

Question 44

What is vibrio cholerae?

Answer 44

Motile gram-negative bacteria that inhabits lakes, rivers, etc. Most of the strains rarely cause disease. It can swim freely or form biofilms on small crustaceans.

Question 45

What makes vibrio cholerae so pathogenic?

Answer 45

Pathogenic strains contain pathogenicity islands, regions that encode cholera toxin (CT), toxin-coregulated-pilus (TCP). CT coded by part of the genome of a fikamentous phage

Question 46

How do vibrio cholerae transfer pathogenicity?

Answer 46

Transfer pathogenicity islands to other vibrios via transformation or transduction. CTX phages carry the pathogenicity islands, phage gets inserted into V. cholera genome. V. cholera genome now has the ability to produce CT and TCP. TCP mediates bacterial aggregation and helps V. cholerae colonise the intestine lining. LPS are the out membrane of vibrios and determine if they are resistant to phages.

Question 47

What does the cholera toxin induce?

Answer 47

Efflux of water into the lumen of the intestine, which causes watery diarrhea.

Question 48

What role does adenylyl cyclase play with vibrio cholerae?

Answer 48

Continuous activation of adenylate cyclase fills cells with cAMP and chlorine is pumped into the lumen. Water follows the direction of the Cl- gradient.

Question 49

Has Cyanobacteria and plant symbiosis evolved?

Answer 49

Yes

Question 50

How doe aliivibrio fischeri and squid have a symbiotic relationship?

Answer 50

Squid provides nutrients for bacteria, bacteria provides luminescence protecting squid from predators.