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Lately there's been a lot of discussion around the many non-human cells essential to a healthy human body — called the microbiome, or metagenome. Much of this is in the gut microbiome. See this question, for example.

The Human Microbiome Project at NIH emphasizes we are just beginning to measure the specifics of this for the human case.

I assume this is similarly true for all mammal species, and I don't know how much farther. Fish have a fairly different body plan than mammals, including a fairly different gut. And coelenterates have an even more different body plan in many ways, again including the gut.

Does a typical fish depend on as large a microbiome as a human? Is there much known about that? What about jellyfish?

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There are multiple parts to an answer for this.

1) There is not only a microbiome in the gut. So microbiomes in general are very diverse. A fish microbiome on the scales will of course be very different to the one on a human skin.

2) Gut microbiomes are also quite different both in taxonomic and functional content, as they are in different ecological niches.

3) There are microbiome studies for nearly every type of organism I could imagine now. Fish, insects, snakes, you name it. They differ in diversity and composition of their microbiome, but also the used methods and databases do differ, so it is hard to compare them.

4) The further away from well studied microbiomes we get, the less specific will be our assignment of taxonomy and function, because we have not seen enough comparable microbes before. So more information will be hidden in the "dark matter" (in metagenomics: reads not assigned to a taxon and/or function).

Unfortunately I don't know of any jellyfish microbiomes so far. Their body (as far as I know ) seems to be much more "permeable" for sea water (-> their environment) and thus I would think that they generally would have aquatic bacteria in whatever corresponds to their gut. The sea microbiome is said to be very diverse and far too little studied, although there are cool projects like the Global Ocean Sampling Day to try and close this huge gap as best as possible.

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  • $\begingroup$ Fish scales are an interesting example to think about. It seems pretty likely that some of the microbiota on the scales are clearly essential to healthy function (once you understand what they are really doing), and others not at all important for good or ill. It could be a hard problem to figure out the difference between metagenome and plain old parasitism or mere proximity. $\endgroup$ – Colin McLarty Feb 8 '17 at 15:35
  • $\begingroup$ @ColinMcLarty I think you are misinterpreting the term metagenome. It does not exclude parasites or only include species essential to health. If it lives in your X (gut, mouth, urinary tract, skin ...) it's part of your X metagenome. $\endgroup$ – Charles E. Grant Feb 9 '17 at 0:48
  • $\begingroup$ @CharlesE.Grant Ah. In fact looking at en.wikipedia.org/wiki/Metagenomics I see it was not originally an organism that had a metagenome at all, but an environment--say a dirt sample, a stream, or a human gut. That article suggests many people still use the term that way. But NIH has their project on "the human metagenome." $\endgroup$ – Colin McLarty Feb 9 '17 at 2:07
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    $\begingroup$ @ColinMcLarty, Its the same usage. It's just considering an entire organism (humans) as the environment. $\endgroup$ – Charles E. Grant Feb 9 '17 at 2:16

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