Microbiome

Question 1

Define microbiome

Answer 1

The collective genes, genomes, and products of the microbiota and the environment
- includes bacteria, fungi, viruses, archaea

Question 2

Components of the microbiome

Answer 2

• The microbiota
• Environmental conditions
• “Theatre of activoty”

Question 3

Microbiome “Theatre of activity”

Answer 3

Polysaccharides
Lipids
Peptides/proteins
Microbial metabolies
Nucleotides

Question 4

Dynamics of the human microbiome varies by:

Answer 4

Body site
Age
Host genetics
Condition
Environmental exposures

Question 5

2 questions when assessing the microbiome

Answer 5

What microbes are present

What can the microbes do

Question 6

What microbes are present looks at the

Answer 6

• taxonomic classification
• communuty composition
• changes over time

Question 7

What can the microbes do looks at

Answer 7

Functional classification of the genetic component to predict activity and metabolic pathways

Question 8

Most often reported taxonomic ranks

Answer 8

Species, genus, family

Question 9

Microbiome profiling methods

Answer 9

Amplicon sequencing
Shotgun metagenomic sequencing

Question 10

Amplicon sequencing

Answer 10

targeted method that uses PCR to amplify and sequence specific regions of a genome, such as genes or gene fragments.

Usually the 16S rRNA variable region

Question 11

Shotgun metagenomic sequencing

Answer 11

Sequence short sequence fragments of all present DNA and then assemble/align.

provides a comprehensive view of the entire microbial community and its functional potential

Question 12

Alpha diversity

Answer 12

Diversity within a single sample

Question 13

beta diversity

Answer 13

Similarity/dissimilarity between samples/over time

Question 14

How does the vaginal microbiome change over the course of pregnancy

Answer 14

Relatively stable through from the first to third trimester, significantly different postpartum, with greater alpha diversity.

Question 15

Which body site has the greatest diversity compared to others (greatest beta diveristy)

Answer 15

The gastrointestinal or oral areas

Question 16

why is the vaginal microbiome unique

Answer 16

It has the lowewst phyla diversity, but the greatest metabolic pathway diversity

Question 17

How do we profile the microbiome function

Answer 17

Look at the -omics

Question 18

Transcriptomics

Answer 18

What genes are being expressed

Question 19

proteomics

Answer 19

What proteins are being produced

Question 20

metabolomics

Answer 20

What metabolic activities are being carried out

Question 21

Multi-omics

Answer 21

Integrate multiple omics approach to better understand the microbiom

Question 22

Comparison for microbiome function

Answer 22

the metagenomic data with the metatranscriptomic data - who is here and at what abundance, and what is actually being done?

Question 23

Kochs postulates

Answer 23

1 - the microorganism must be found in diseases individuals but not health.
2 - the microorganism must be cultured from the diseased individual
3 - inoculation of a healthy individual with the cultured microorganism must recapitulate disease
4 - the microorganism must be reisolated from the inoculated, diseased individual and matched to the original organism

Question 24

Traditional Kochs postulates IBD

Answer 24

1 - Identify and isolate
2 - culture in lab
3 - Inoculate to determine a causal role
4.- Isolate from the diseased model

Question 25

Ecological Kochs postulates Disease causing communities

Answer 25

- Identify and isolate the community - Transfer to recapitulate disease - Isolate the community from the disease model

Question 26

Modified Kochs postulates Health promoting microbes

Answer 26

- Identify and isolate the beneficial microbe associated with healthy outcomes - Culture in lab - Inoculate in an animal IBD model to determine a protective role against disease (reversion) - Isolate the beneficial microbe from the animal model.

Question 27

Lactobacillus dominance

Answer 27

Protects against adverse sexual and reproductive health outcomes

Question 28

Vaginal dysbiosis

Answer 28

Higher bacterial numbers, higher bacterial diversity, higher pH. Polymicrobial, clue cells, coccobacilli, gram variable, few/absent lactobacilliq Bacterial vaginosis

Question 29

Optimal vaginal microbiome

Answer 29

Low alpha diversity Lactobacilli are common and there are few to no other organisms

Question 30

Temporal fluctuations in the vaginal microbiome

Answer 30

Due to sexual activity, cleansing practices, antibiotics

Question 31

Protective mechanism of vaginal lactobacilli

Answer 31

Production of L-lactic acid by glycogen breakdown selects for acid tolerant bacteria and the suppression of other endogenous bacteria. Contributes to a noninflammatory environment.

Question 32

L-lactic acid vs D-lactic acid

Answer 32

Human cells and all vaginal lactobacilli produce L-lactic acid

Question 33

How do we know lactic acid production is important

Answer 33

Human vaginal samples - Metabolomics, pH, transcriptomics, proteomics In vitro testing - Lactic acid production by VL, testing antimicrobial activity against viral pathogens

Question 34

What do high LDH levels correlate with

Answer 34

Epithelial intercellular junctional protein levels The expression of genes relevant to barrier integrity and the expression of junctional proteins.

Question 35

Other ways vaginal lactobacilli protect against STIs and BV

Answer 35

Bacteriocins - pathogen inactivation Lactic acid - pathogen inactivation, vaginal acidification, barrier maintenance Adhesion to epithelium - spatial competition, receptor expression alterations

Question 36

Pathogenic mechanism of BV-associated bacteria

Answer 36

Biogenic amines - odour Host degrading enzymes - abnormal mucus, disrupted epithelial barriers Tissue adherent biofilm - persistence

Question 37

Biogeography of the gut microbiome

Answer 37

Bacterial load increases, O2 decreases, pH increases, and mucus type and thickness increases as you move towards the rectum

Question 38

What are the most abundant bacteria in most individuals

Answer 38

Bacteroidetes, firmicutes

Question 39

Bacteria in the small intestine

Answer 39

More sugars are absorbed and it is more acidic - there is less bacterial diversity and abundance

Question 40

Bacteria in the large intestine

Answer 40

More complex carbs (fibers, mucus) available, higher bacterial abundance and diversity and a thick mucus layer covering the epithelium.

Question 41

Colonisation resistance in the gut

Answer 41

The ability of the gut microbiota to provide protection against infection

Question 42

Impaired colonisation resistance is caused by

Answer 42

Environmental and behavioral factors such as antibiotic usage and diet

Question 43

Effect of a fiber free diet

Answer 43

Increase in mucin-degrading bacteria, thus a decrease in the mucus layer and the susceptibility to enteric pathogen infection

Question 44

mechanisms of active antagonism in gut microbiome colonisation resistance

Answer 44

T6SS, release of bacteriocins, pheromones

Question 45

Other mechanisms in gut microbiome colonisation resistance

Answer 45

Nutrient or space competition Active antagonism Inhibitory metabolites