GI tract functionality
15 important questions on GI tract functionality
What information do you get from the 16s rRNA
How can you see if a micro-organism is still alive?
By adding a probe that will bind to DNA only if the membrane is not intact, so the micro-organsim will be dead.
What are commensal relationships?
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What are the short chain fatty acids?
- acetate
- butyrate
- lactate
- propionate
Where do you find B. longum, L. plantarum and Ba. theta?
L. plantarum you find in the small intestine.
If you look at the genome there is a part available that looks like the product that is present in the small intestince for L. platarium and in the large on for the other 2.
SO the genome can product the function of the bacteria. But not all the things that are incoded have to happen.
How can you predict what the micro-organism will be doing?
How is the influence of a microbe on the gut researched?
By germ-free animals
You can maked compairesens in a controled way and you can also look at interactions.
Unfortunately there are so many other microbes present in real life that it is hard to predict something.
What does a DNA microarray for gene expression do?
You grow the microorganism under 2 different conditions.
Isolate the RNA and add it to the microarray.
Now you will see which genes are expressed.
red only situation 1
green only situation 2
yellow bought situations
What kind of study did they do to compare what dna was activated in the intestine?
What did they do and see when they compaired mouses with and without intestinal microbes?
It was found that microbes:
- Improve host nutrient absorption and processing
- Increased micronutrient absorption
- Improved barrier function of epithelial cells
- Alteration in host capacity to metabolize xenobiotics and endogenous toxins.
- An instructive role in postnatal intestinal maturation.
What did they see in a difference of diet between mices?
Simple suger diet: Expression of genes involed in utillization host mucus glycans. So they quicly adapt and start using the glycans of the muces.
How does the data analyses of metagenomics go , what is a advantage and what is a disadvantage?
The conclusions that you make will be based on apart of the genes. Not the whole gene.
So you can say my population has these genes and will do this. Not specie.
So methagenimic libaries contain the collection of genomes/genes form microbes in an environment and the function of these collected genes. can subseqently be determent.
A disadvantage of the metagenomic libaries is that hese have to be very large in order to get a reasonable coverage of the genetic diversity.
What was the conclusion of this data set?
In which sick people, people form spain and people form denmark were plotted?
Therfore it is expected that certain people have one certal microbe that is in comunication with other microbes and all in all performs the same function. But they have a different micro flora for it.
What do you determine what microbes are they, what are they doing and what is the genetic potential (metagenomics, metatranscriptomics, metaproteonics)?
- SSU rRNA approaches
What are they doing:
- metatranscriptomics: based on RNAs
- metaproteomics: based on proteins
- Metabonomics: based on metaolites
What is the genetic potiential:
- Metogenomics: based on DNA
What is the extra dimension of complexity wit metratrancriptomics/metaproteomics?
- Gene expression level went up
- Gene expression is the same but the population level went up
- Or a combination of the 2
So also do a DNA aproach to see if there is realy a change in comunity or expression.
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