Split: Gut Microflora

[S.A.M.]

Just to clarify, rRNA sequences are diagnostic to specific species. DGGE is a quicker but less specific method to assess the population. rRNA is reversed-transcribed, usually subjected to nested PCR. In the end you got PCR products of a conserved region of the rRNA-gene which differs in few bases from species to species. This affect the melting behaviour of the resulting PCR products, which can be monitored in a denaturing gel. Unless you already know what populations exist a DGGE can not be used to unambigously identify the underlying species, though. In any case it is a well-known fact that diets change the gut flora (the working principle of pre-biotic foods).

So much for the technical aspect. Now regarding the often repeated "no bacteria no life phrase used in this thread". In a way this is correct. The ecosystem would collapse without bacteria (in fact the atmosphere was shaped by bacteria). Also, eukaryotes would not exist (mitochondria). However, sterile organism can live on without gut or other bacteria, provided that they are protected from infections.
Also the assumption that the present bacteria are the same as billions years ago is absolutely stupid. The first bacteria were likely to be anaerobic extremophiles which are now living for the most part restricted to certain niches. Now the majority of pioneer bacteria are aerobes, for examples, which of course did not exist since the first photosynthetic bacteria evolved.

In fact you can see the little bugger changing over time even if you freeze them for a prolonged time.

just my 2 cents.

Thanks for the explanation.

I wondered about the effects of freezing, since most clinical studies, inspite of collecting fresh samples, only process them at later dates after freezing.

I also wondered if experiments in animals took account of coprophagia.

Could you hazard a guess as to why individuals on the same diet would produce different populations of micorflora? I'm been cracking my brain trying to think where individual differences would come to play.

Would the length of intestines (assumed to be longer in vegetarians) make a difference? Anything else?

 

[CharonZ]

Sam:

I wondered about the effects of freezing, since most clinical studies, inspite of collecting fresh samples, only process them at later dates after freezing.

Depends on fast it is done. Usually freezing in liquid N2 should not change the community significantly. But isolating a sample and sending it to somewhere (especially minimally or even not cooled at all), can make a big difference.

I also wondered if experiments in animals took account of coprophagia.

What experiments do you have in mind?

Could you hazard a guess as to why individuals on the same diet would produce different populations of micorflora?

There are in fact different possibilities. Genetic disposition, for instance. A simple (but extreme) example. Lactose intolerant people for instance do not digest lactose, which then become available for certain bacteria, resulting in changes in the community. Also exposure to different bacteria can be a reason. I would assume that identical twins grown exactly the same way (under sterile conditions) and eating the same diet (and same amount of everything, of course), should have more or less similar communities. Even then it is not absolutely sure, of course, as the bacteria can interact with each other and by pure chance some might outcompete others. Certain genetic elements might spread in certain subpopulations, or random mutations can result in the change of fitness of certain species and so on. Despite everything the gut is a quite fluctuating environment.
One should note, though that despite all the minute differences in the composition between individuals the biota should not exhibit gross changes. You tend to find similar genera in all humans, if in different abundances.

The reason is thatthese have adapted to a life in the gut (or rather certain areas of the gut) and most other bacteria that one might ingest will most likely not get a good foothold in there. I assume that the highest differences will be observed among the low abundance bacteria.

Would the length of intestines (assumed to be longer in vegetarians) make a difference? Anything else?

I would not think that the length by itself would be huge difference unless it creates gradients or conditions different from a short one. In this particular case I'd assume that the differences in available nutrients for the bacteria will have a larger impact. This is just my (unreferenced) opinion, though.

 

[S.A.M.]

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