A “microbiome” is all the microbes (bacteria, fungi, viruses and their genes) living in a specific environment, and how they all interact with each other. Animals have several microbiomes. There’s an oral microbiome (the mouth and all the microbes in it), as well as nasal, respiratory, rumen, intestinal, vaginal, rectal and skin microbiomes. The various microbiomes interact with each other as well as the host animal.
Animals are outnumbered by these microbial tenants. I call myself a human, but most of me isn’t. If I could separate all the cells in my body into a pile of human cells and a pile of microbial cells, the pile of microbial cells would be biggest. That’s also true of you, and it’s even more true with cattle, because the rumen and large intestines are giant microbial fermentation vats.
The key point about the “microbiome” is that the microbes and animal cells interact with each other and the environment they’re in. That’s most obvious when microbial populations are imbalanced. Bovine respiratory disease, rumen acidosis, bloat and liver abscesses are all examples of an out-of-kilter microbiome.
Dietary changes can temporarily shift microbial populations, but permanently changing an established microbiome is very challenging. That’s one reason why so many commercial probiotics intended to “fix” or improve the microbiome need to be fed continuously (and have inconsistent results).
It may be more effective to intervene early in life, while the various microbes are still sorting themselves out. That’s where much of the microbiome research is currently focused.
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