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PHAR 510 > Lecture 7 - Microbiota > Flashcards

Lecture 7 - Microbiota Flashcards

1
Q

number of microbial genes vs human genes

significance?

A

2-20 million microbial genes vs 20,000 human genes

therefore the bacteria have genes for things we cannot do

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2
Q

3 functions of bacteria in the microbiome

A
  1. maturation of immune system and gut physiology
  2. synthesis of vitamins and metabolites
  3. digesting of complex glycans derived from food (fibre)
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3
Q

when does the microbiota contribute to disease?

A

when the gut microbiome is IMBALANCED –> disease

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4
Q

why are we just discovering the involvement of microbiome in disease now?

A

genetic tools have helped us understand the complexity of the microbiome

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5
Q

3 general methods for studying structure and function of microbiota

A
  1. STRUCTURE (ex. 16S rRNA gene sequencing)
  2. FUNCTIONAL POTENTIAL (what can they do? ex. single cell genome sequencing)
  3. IN SITU FUNCTION (what are they doing? ex. metabolomics/proteomics/transcriptomics)
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6
Q

why do we look at 16S rDNA?

A

phylogenetic marker found in all species to identify bacteria

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7
Q

describe the 16S rDNA gene

A

some regions are conserved, some regions are more variable so can identify specific bacteria

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8
Q

bioinformatic methods for human microbiome profiling

A

whole genome sequencing –> looking at all DNA in a sample and compare to reference genome or find general functions of genes to see role of bacteria

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9
Q

how do we acquire our gut microbiota?

A

food, environment, at birth

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10
Q

what is an issue with microbial studies?

A

if you use PCR, will always see something but may not be truly there

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11
Q

does environment or genetics play a bigger factor in shaping the human gut microbiota?

A

environment

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12
Q

2 types of diversity we can look at

A
  1. alpha
  2. beta
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13
Q

alpha diversity

A

within 1 sample, how diverse the bacteria are

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14
Q

beta diversity

A

compare diff samples

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15
Q

what is Bray-Curtis dissimilarity?

A

non-phylogenic (does not consider taxonomy) beta diversity which takes into account the abundance

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16
Q

what is the UniFrac distance between a pair of samples?

A

fraction of unique branch length –> ratio of unique branch length that only leads to OTUs in sample A or B VERSUS total branch length in either sample

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17
Q

purpose of UniFrac

A

to compare differences based on phylogeny and genetic background

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18
Q

what does UniFrac show if samples are IDENTICAL?

A

unique branch length is 0 so UniFrac distanc is 0 btwn samples

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19
Q

what does UniFrac show if samples are COMPLETELY DIFFERENT?

A

UniFrac distance is 1 btwn samples

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20
Q

what does UniFrac show if samples are INTERMEDIATELY SIMILAR?

A

UniFrac distance is 0.5 btwn samples

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21
Q

Unweighted vs weighted UniFrac

A

unweighted is qualitative measure of diversity that does not consider the abundances of OTUs

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22
Q

describe Principle Component Analysis

A

extracts the most important information to reduce the size and complexity of the data set

computes new variables called PRINCIPLE COMPONENTS which are linear COMBINATIONS of the original variable

23
Q

2 components in PCA

A
  1. required to have the largest possible variance to explain/extract the largest part of variance from the data
  2. orthogonal to the first component and to have the largest possible inertia
24
Q

describe the microbiome throughout life

A

becomes more diverse and stable

25
Q

how does the diversity in phylogeny of microbiome relate to the functional diversity in microbiome?

A

see varying taxonomy of bacteria in samples but the functionality of the bacteria involved is the SAME across samples –> therefore phylogeny doesn’t tell you about genetics

26
Q

what drugs affect microbiota?

A

many, even the non-antimicrobial ones!

27
Q

which drugs have the largest impact on gut microbiota?

A

PPIs

28
Q

how do PPIs affect gut microbiota?

A

PPIs affect pH in stomach which affects metabolism and pH in the gut and allow MORE bacteria to colonize

29
Q

how do SSRIs affect gut microbiota?

A

some specific bacteria are reduced in ppl taking SSRI (later found that these bacteria have serotonin receptor so can metabolize serotonin)

30
Q

how does Metformin affect gut microbiota?

A

microbiome may contribute to positive impact of metformin?

31
Q

how do non-antibiotic drugs affect growth of bacteria in vitro?

A

many non-antibiotic drugs that should have human target also inhibit growth of bacteria –> this could be how they affect the microbiome

32
Q

what type of bacteria are typically in microbiome?

A

most bacteria in microbiome are ANAEROBIC

33
Q

2 products of microbiome metabolizing our food

A
  1. short chain FA
  2. secondary bile acids
34
Q

3 examples of short chain FA produced by microbiome metabolizing our food

A
  1. butyrate
  2. propionate
  3. acetate
35
Q

why is it important that microbiome produces butyrate?

A

feeds colonocytes to maintain anaereobic environment bc it consumes O2 from blood

36
Q

large impact of the short chain FA?

A

have direct effect on gene expression in immune cells

37
Q

how are secondary bile acids made?

A

produced from primary bile acids made by liver and end up in large intestine

38
Q

how do bile acids affect our body?

A

can influence metabolites and the intestinal niche, reducing C. diff infection

39
Q

when does dysbiosis occur?

A

antibiotics or poor diet

40
Q

what happens to microbiota diversity in dysbiosis?

A

reduced diversity

41
Q

what is the consequence of the microbiota having reduced diversity?

A

allows for bloom of pathogenic proteobacteria that can survive in aerobic environment

this affects metabolism and reduces short chain FA leading to inflammation, reducing anaerobic environment to favour proteobacteria

42
Q

why is antibiotic use considered a 4-edge sword?

A
  • cures infection
  • protects community against infectious disease
  • resistance
  • microbiota disruption
43
Q

how can we optimize our use of antibiotics?

A
  1. use more narrow spectrum antibiotics that kill certain bacteria and spare the microbiome
  2. target virulence factors
  3. have better diagnostics to know which bacteria is causing infection
44
Q

describe the relationship btwn taking antibiotics and cancer immunotherapy

A

cancer patients undergoing immunotherapy who were also taking antibiotics did NOT respond well to the immunotherapy

45
Q

what happens if mice receive a stool sample from a cancer patient who DOES respond to immunotherapy?

A

mice will respond better to immunotherapy

46
Q

describe survival in ppl taking antibiotics with immunotherapy

A

worse survival than ppl not taking antibiotics

47
Q

2 methods for colonization resistance against intestinal pathogens

A
  1. immune system/host factors
  2. direct interactions
48
Q

how do interactions with immune system prevent colonization?

A

Can stimulate release of antimicrobial factors like IgA and regIIIy

49
Q

how do direct interactions of microbiome with pathogen prevent colonization? (3)

A
  1. compete for food
  2. producing antimicrobial factors
  3. using T6SS to inject other bacteria with toxin
50
Q

consequences of antibiotic use on pathogen infection

A

antibiotics mess up the microbiota and allow for more colonization and more severe infection by pathogenic bacteria

51
Q

consequences of antibiotic use in C. diff infection

A

antibiotics will DEPLETE the microbiota and allow C. diff to colonize bc it is resistant to antibiotics –> then C. diff will produce toxins and cause pathogenesis

52
Q

how does a healthy microbiota normally protect you from C. diff?

A

microbiota will produce bile acids

53
Q

describe what happens when you treat C. diff with vancomycin

A

C. diff is not resistant to vancomycin so will be killed BUT microbiota will be depleted and become MORE SUSCEPTIBLE to C. diff again –> stuck in re-infection loop

54
Q

describe the microbiota diversity in recurrent C. diff patients

A

poor microbiome diversity

PHAR 510 (11 decks)

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