Lecture 7 Human microbiome Flashcards
Defenition of the microbiota?
The ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space (and have been ignored as determinants of health and disease) - Joshua Lederberg, 2001
Definition of the metagenome?
The collection of genes that are encoded by the members of a microbiota
Definition of the microbiome?
The entire habitat, including the microorganisms, their genomes (i.e., genes) and the surrounding environmental conditions (based on “biome”) = the microbiome
When did microbiome research advance?
Microbiome research advanced by development of DNA sequencing technology (cultivation-independent methods)
By sequencing of what component is microbiome analysis done?
16S rRNA amplicon sequencing
What factors make the colon a niche for bacteria?
- temperature
- digestion (fibers)
- acidity: in the colon the pH is close to neutral (further down the channel)
- transit time (time for food to go through the intestine)
- metabolites are absorbed by the colon (no inhibition of growth bc of compounds)
What do the bacteria in the gut contribute to ?
- Colonization resistance: pathogens have no chance to colonize
- Food digestion
- Synthesis of compounds, including vitamins
- Brain-gut axis
- Immune system
What is a drawback when secuencing the microbiota composition with 16s rRNA?
- Microbiota composition analysis by 16S rRNA amplicon sequencing: reading sequence of variable parts. However, you are comparing the sequence with a database, so new micro-organisms cannot be discovered.
What method was used before this? Advantages?
-> Before this: cultivation. Can add specific substances: change the environment: selective conditions/growth. Select one specific organism.
What are other drawbacks of sequencing?
Other drawbacks: you don’t know what organisms are alive or dead. Price is also a limitation. Certain resolutions: identification on genus/species levels/different taxonomic levels. But, there are also different strains which are important: goes beyond species.
Total microbiome DNA seq vs 16s rRNA seq: what more can you discover?
- Genes
- Variants
- Polymorphisms
- Functional information
What are the 3 enterotypes of the Enterotypes of the human gut microbiome?
1) Bacteroides
2) Prevotella
3) Ruminococcus
The Bacteroides ecosystem consists largely of bacteria that get energy by fermenting sugars and proteins. The Prevotella ecosystem contains a lot of microbes that like to dine on proteins in the mucusy lining of the gut. Mmmm. Ruminococcus, with its vague echo of cows, happens to be the most common. The residents of this ecosystem dine on those gut mucus proteins, but they also enjoy simple sugar treats
What are Koch’s postulates?
De ziektekiem moet in ongewoon grote hoeveelheden in de patiënt of plant worden aangetroffen maar niet in het gezonde dier of plant.
De ziektekiem moet kunnen worden geïsoleerd en verder gekweekt.
Een proefdier of dezelfde soort plant dat met de gekweekte kiem besmet wordt, moet dezelfde ziekte krijgen.
De ziektekiem moet uit het proefdier of de proefplant geïsoleerd kunnen worden, en moet gelijk zijn aan de ziektekiem in het lichaam van de patiënt.
Waar profiteren bacteriën van die sporen kunnen vormen?
Spore-forming properties: help bacterium survive/become antibiotic resistant
When losing weight as an obese person, the no of Firmicutes bacteria became (more/less) and Bacteroidetes became (more/less)
Fermicutes: less
Bacteroidetes: more
