Lecture 8 - Manipulating the Microbiota

Question 1

3 characteristics of disease-associated microbiota

Answer 1

1. reduced diversity
2. reduced metabolism
3. reduced O2 –> increased anaerobes

Question 2

3 methods to convert disease-associated to homeostastic microbiome

Answer 2

1. FMT
2. probiotics
3. prebiotics

Question 3

2 characteristics of health-associated microbiome

Answer 3

1. increased CD8+ T cell stimulation
2. altered metabolic profile

Question 4

3 ways that homeostatic microbiome is converted to health-associated microbiome

Answer 4

1. drugs
2. probiotics
3. prebiotics

Question 5

is it easier to convert from disease-associated to homeostasis OR homeostasis to health-associated? why?

Answer 5

easier to convert from disease-associated to homeostasis

homeostatic microbiome is already established so harder to leave this state

Question 6

when can C. diff infect microbiome?

Answer 6

when there’s loss of diversity –> C. diff can develop

Question 7

how does C. diff damage GIT?

Answer 7

releases toxins that damage epithelial cells

Question 8

why do most antibiotics not work for C. diff?

Answer 8

naturally resistant

Question 9

usual treatment for C. diff and consequence

Answer 9

antibiotics that can kill C. diff –> but this will continue depleting microbiota making them even more susceptible to infection after treatment

Question 10

what is a better treatment than antibiotics for C. diff?

Answer 10

FMT

Question 11

is FMT only helpful for C. diff infection?

Answer 11

no, also helps other bacteria!

Question 12

other bacterial infection that can be treated with FMT?

Answer 12

vancomycin-resistant enterococcus

Question 13

describe FMT in allogeneic hematopoietic stem cell transplant

Answer 13

• microbiome is compromised in HPSC transplant and becomes susceptible to other infections
• did autologous FMT and microbiome returned to normal

Question 14

what is autologous FMT?

Answer 14

stool sample before antibiotics, then give back stool after treatment

Question 15

when is autologous FMT helpful?

Answer 15

when you know a treatment will severely mess up microbiota

Question 16

benefit of FMT

Answer 16

straightfoward

Question 17

4 downsides of FMT

Answer 17

1. standardization issues
2. safety issues
3. colonization issues
4. administration

Question 18

why is standardization an issue with FMT?

Answer 18

cannot standardize! samples always different

Question 19

what are the safety concerns with FMT?

Answer 19

1. don’t know what you’re transplanting (don’t know all microorganisms)
2. unclear what is a “healthy” donor

Question 20

what are the colonization issues with FMT?

Answer 20

microbiota has been wiped out so the new microorganisms will colonize but might not actually colonize! the transplanted bacteria may be taking up space and preventing new bacteria from developing –> less diversity

Question 21

issue with commercial probiotics

Answer 21

bacteria survive GIT and then get excreted –> rarely colonize host

Question 22

diversity in microbiome after antibiotic treatment:

FMT vs nothing vs probiotics

Answer 22

FMT: microbiota diversity returned to what it was before antibiotics

nothing: takes longer to return but eventually returned to what it was before antibiotics

probiotics: diversity never returns to what it was before antibiotics

Question 23

why might probiotics help C. diff? (3)

Answer 23

1. bacteria can modify bile acids to make SECONDARY bile acids that inhibit C. diff germination
2. bacteria will anti-bacterial components
3. bacteria will compete for nutrients

Question 24

what type of drugs are most helpful for recurrent C. diff infection?

Answer 24

live bacteria therapeutics

Question 25

3 examples of live bacteria therapeutics for C. diff

Answer 25

1. SER-109 (purified fecal samples that can displace C. diff)
2. VE303 (8 live bacteria)
3. RBX (first approved microbiome drug!)

Question 26

why did live bacteria therapeutics fail as cancer treatment? (2)

Answer 26

issues with colonization
1. could not force exogenous bacteria to grow in patient
2. did not have correct mix of bacteria

Question 27

describe the use of a synthetic microbiota

Answer 27

rather than FMT, collect isolate bacteria and put together as a mix that could resemble microbiome

Question 28

is a single species of bacteria sufficient to correct microbial damage and infection/

Answer 28

no!! diversity is important

Question 29

describe why diversity is important for preventing vancomycin-resistant enterococcus infection

Answer 29

• 2 bacteria inactivate the antibiotic, allowing growth of another bacteria
• this bacteria allows the growth of another bacteria
• this bacteria inhibits VRE

Question 30

describe vaginal microbiota

Answer 30

mainly has H2O2-producing lactobacilli which suppresses growth of opportunistic pathogens

Question 31

what happens in bacterial vaginosis?

Answer 31

increased anaerobic bacteria and loss of lactobacilli –> with treatment, will have recurrent infection

Question 32

how do we digest complex fibres?

Answer 32

we do not have enzyme to digest these, so bacteria in large intestine have enzymes that break down fibres and ferment to use as carbon source

Question 33

why is the digestion of complex fibres helpful for bacteria?

Answer 33

helps them maintain diversity

Question 34

what are prebiotics?

Answer 34

complex fibres

Question 35

why does human milk have oligosaccharides if we do not have enzymes to digest?

Answer 35

doesn’t actually nourish the baby but will support bacteria in their microbiome

Question 36

what happens to C. diff infection with increased fibre diet / prebiotics?

Answer 36

reduced C. diff colonization

Question 37

how do gram negative pathogens interact with their environment?

Answer 37

pili on their surface

Question 38

how does UPEC attach to host cells?

Answer 38

FimH

Question 39

what is FimH?

Answer 39

an adhesin at tip of pili that binds mannose

Question 40

what happens with a FimH antagonist?

Answer 40

displaces bacteria so they excreted –> helps UPEC (UTI)

Question 41

Why are mannosides helpful?

Answer 41

interfere with FimH to prevent recurring UTIs

Question 42

role of FimH in IBD / Crohn’s Disease

Answer 42

invasive E. coli and other bacteria bind to gut wall via FimH to cause inflammation