Microbiota

Question 1

What is part of the microbiota?

Answer 1

• fungi
• protista
• Eubacteria
• Archaebacteria

Question 2

Microbiota determination by culture

Answer 2

• most bacteria strictly anaerobic
• probably 80% of gut commensals are not cultivatable
• isolation is important

Question 3

Microbiota determination by 16S rRNA amplicon sequencing

Answer 3

• universal 16S rRNA primers available
• cheap
• high resolution

Question 4

Microbiota determination by shotgun metagenomics

Answer 4

• good recovery of bacteria
• almost unbiased
• full genetic information

Question 5

α-diversity

Answer 5

taxa variation in one sample

high alpha-diversity should support stability and health

Question 6

β-diversity

Answer 6

diversity between different samples

Question 7

functions of the gut microbiota

Answer 7

1. metabolic: fermentation
2. trophic: short chain fatty acids, lactic acids, vitamins
3. protective: direct inhibition of pathogens, fortification of barrier function
4. immunological: innate immune training, adaptive immunity, tolerance

Question 8

Sampling of lung microbiota

Answer 8

• sputum: bronchi; hard to get a control
• BAL: bronchi & bronchioles; unpleasant
• bronchoscopical brush: like BAL
• tissue: target tissue; control is adjacent tissue (might be affected by microbiota)

Question 9

Why is the gut-lung axis important

Answer 9

diet has an impact not only on the gut microbiota but alas on the lung microbiota

Question 10

study design problems

Answer 10

hen & egg problem:
1. what is the baseline?
2. does disease/treatment effect microbiota?
3. does the microbiota determine the outcome?
4. does disease/treatment destroy resilience?

Question 11

What are the four types of mice used for animal experiments?

Answer 11

1. wild/petshop mice: high α-diversity, can contain facultative pathogens
2. specific pathogen free (SPF): lab standard, pathogen free, monitored health
3. gnotobiotic mice: contain defined bacteria (introduction of bacterial isolates in germfree mice
4. germfree mice: no bacteria on any body surface

Question 12

What is the breeder effect?

Answer 12

depending on the breeder/seller of the lab mice the susceptibility to certain pathogens is different. it can also effect the cell count of T cell (Th 17)

Question 13

development of the microbiota

Answer 13

• in humans microbiota is mainly settled during the first year
  
  • breast feeding is one major factor (contains prebiotic commensals, immune mediators, IgA)

Question 14

microbiota manipulation

Answer 14

probiotics:
- beneficial bacteria
- contained in yogurts, etc.

prebiotics:
- non-digestible food compounds that support beneficial bacteria growth

fecal transplantation