It is the initial purpose of a microbiome to be at least commensal, in that it is usually prohibitively expensive to maintain a sterile environment so the odds of a true pathogen colonizing a system is greatly reduced if you simply have a crowded space of neutral participants.

Once that's true it does seem there's a lot of host and microbiome interactions we've only begun to explore, but it shouldn't be surprising that co-evolution of the microbiome and host begins to take over as soon as you have one. One great example is short-chain-fatty-acid (SCFA) producing bacteria in the human gut. [1] These seem to be essential, and if there was a general takeaway to improve health, it would be to eat your roughage so they can do their job.

This is also why high alpha-diversity (community richness in particular) is such a dead-ringer for healthy vs diseased states. And frustratingly, is often exactly where the story ends for a lot of observational studies.

Also, in case you are curious, artificially sterile mice (gnotobiotic mice) tend to act differently than other mice, which is pretty odd to be honest, and why the gut-brain axis is a plausible mechanism to research further. [2]

[1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC10180739/ [2]: https://www.sciencedirect.com/science/article/pii/S088915912...