I remember in my Microbiology class how an animal’s microbiota is very important to its health (this also applies to fungi and plants). I distinctively recall how Professor Bei Nan emphasized the difference between microbiota and microbiome, which are often confused even in scientific literature. Microbiota refers to the community of micro-organisms living on or within a larger organisms over a period of time. Microbiome refers to the genetic content of all organisms living within or in a host, and it includes the genetic content of the host organism. Since we are Homos sapiens, the most research has been done on the gut microbiota of humans; two very important bacteria for human microbiota are Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarius subsp. thermophilus (S. thermphilus), which are often found together in yogurt. How is the gut microbiota of other animals different from that of humans? Are there similar micro-organisms found in the gut microbiota of all, or some, animals?
I remember that termites have a microorganism in their guts which help them digest wood. And there are some shrimp that live by deep-sea vents which have a symbiotic relationship with bacteria living on their gills.
I would really like to know the answers to this myself!
I have searched PubMed and others about the impacts of internal species on the (human or other’s) gut. Yeah, a lot of it is over my head, but I think we really just do not have enough scientific data yet to draw many conclusions (despite all the product ads on the internet promising miracles of gut health). It is just super complex.
I remember an old article titled, “You RNA what you eat”, which suggested that individual ways of metabolizing stuff in the human gut was hugely dependent on that person’s genetic makeup and life exposures. …Such that fewer generalities about nutrition and metabolism could be drawn than one might expect, as there are so many different types of people and so much individualism within their guts.
At this point in time and with the state of the art research going on… well, I imagine it will be years before we have a consensus of answers about the human biome, and impressively longer before there is a consensus of gut science on other species.
I would suspect we will learn more about ~economically~ important species (domestic species like cattle and chicken) well before wild species (and perhaps even before we learn about human species 
)
Any plant-eating animal ca do that only because of microorganisms and sometimes organisms inside those microorganisms, termites are known for that chain, but any mammal, bird or reptile eating plants can’t digest it by itself.
Yes, there is a vast range of microorganisms with particular roles and associations/dependencies with particular termite taxa. Apparently termites long ago evolved behavior to systematically pass on their microbiota to their larvae. Here’s a talk by Jared Leadbetter of Caltech who has spent 24 years working to “clarify the relationship between termites and their hindgut microbes”
And here’s a 2002 paper that identifies spirochete bacteria and protists in the gut flora of a 20 million year on termite preserved in amber.
Microbiomes of diverse animals — that is a very long story!
First, as a long-term insect microbiome researcher, I disagree with the microbiome/microbiota distinction in @haemocyanin11 's post. I use these terms interchangeably.
Animals differ dramatically in the abundance, diversity, specificity, transmission, localization, and functions of their symbiotic microorganisms. Many harbor abundant and diverse microbes (bacteria, fungi, protozoa, Archaea) within their digestive tracts, but those colonizing other body surfaces can also be important. Also, invertebrates often host symbiotic microbes within their tissues and cells. Microbial symbionts can aid digestion, produce vitamins and deficient nutrients, remove toxins, protect against parasites and pathogens but also stressors such as heat, affect reproduction, influence development, and affect uncountable other functions. They transmit through the environment, or socially, and in many cases through the female reproductive system, sometimes very reliably for tens or hundreds of millions of years. On the other hand, some animals harbor virtually no microbial symbionts at all.
Two general publications on the animal microbiome that I often recommend and cite:
https://www.pnas.org/content/110/9/3229.short
http://fiererlab.org/wp-content/uploads/2019/07/Hammer_etal_2019_FEMSMicro.pdf
Apologies for any spoilers, but among the things I learned were:
- Some of the hindgut microbes are anaerobic (i.e. poisoned by oxygen), which means they can’t live outside the termite gut and need to stay away from oxygen diffusing from the gut walls.
- The symbiotic lineage of termites and their microbiota goes back more than 100 million years. Basically, these microbes exist because they have been fed by adult termites to their offspring for all that time.
- Digestion of wood fiber is primarily performed by various protozoa (e.g. about 12 species in the termites that Leadbetter studies) and these protozoa are themselves hosts for symbiotic bacteria.
- The protozoa (and enzymes from the termite) convert the cellulose into acetate, which the termite can metabolize. But this process also creates CO2 and H2.
- One possible destination for the CO2 and H2 is for them to be metabolized into methane (CH4) by species of archaea that live on the termite’s gut wall.
- But in many termites, the dominant route for the CO2 and H2 is for them to be metabolized into more acetate by CO2-reducing homoacetogen bacteria.
- A lot of these metabolic steps are accomplished by spirochete bacteria, of which there may be 100 species in a typical termite. Many species (such as Treponema primitia, described by Leadbetter in 2004) are in the genus Treponema which also contains the organisms responsible for various human diseases, including syphilis.
- A related spirochete, Treponema azotonutricium, fixes nitrogen from its surroundings in the gut into protein (presumably amino acids). In that process it consumes some of the hydrogen produced by other processes.
Oh and there’s microscopy video of swimming protozoa and bacteria from termite gut contents!
Thanks @symPiotr, both for the summary of the field and the links to those two overview papers. It was interesting to read that there are plenty of animals that have no need for symbionts.
Let’s not forget ruminants. Their microbiota have been studied perhaps more than some other animals, because they are economically valuable livestock.
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