What is part of the microbiota?
- fungi
- protista
- Eubacteria
- Archaebacteria
Microbiota determination by culture
- most bacteria strictly anaerobic
- probably 80% of gut commensals are not cultivatable
- isolation is important
Microbiota determination by 16S rRNA amplicon sequencing
- universal 16S rRNA primers available
- cheap
- high resolution
Microbiota determination by shotgun metagenomics
- good recovery of bacteria
- almost unbiased
- full genetic information
α-diversity
taxa variation in one sample
high alpha-diversity should support stability and health
β-diversity
diversity between different samples
functions of the gut microbiota
- metabolic: fermentation
- trophic: short chain fatty acids, lactic acids, vitamins
- protective: direct inhibition of pathogens, fortification of barrier function
- immunological: innate immune training, adaptive immunity, tolerance
Sampling of lung microbiota
- 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)
Why is the gut-lung axis important
diet has an impact not only on the gut microbiota but alas on the lung microbiota
study design problems
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?
What are the four types of mice used for animal experiments?
- wild/petshop mice: high α-diversity, can contain facultative pathogens
- specific pathogen free (SPF): lab standard, pathogen free, monitored health
- gnotobiotic mice: contain defined bacteria (introduction of bacterial isolates in germfree mice
- germfree mice: no bacteria on any body surface
What is the breeder effect?
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)
development of the microbiota
- in humans microbiota is mainly settled during the first year
- breast feeding is one major factor (contains prebiotic commensals, immune mediators, IgA)
microbiota manipulation
probiotics:
- beneficial bacteria
- contained in yogurts, etc.
prebiotics:
- non-digestible food compounds that support beneficial bacteria growth
fecal transplantation
