I think there are Nobel prizes for more work here. We know so little about how bacteria affects our bodies and the true roles that they place, despite there being billions and billions of them.
I’m pretty sure if we aren’t careful the same replication crisis that happened in social science will happen here, the interaction of the gut bacteria is so complex it will be very difficult to get consistent results.
I work in a lab where some of the researchers are working on the much simpler fly gut. Even in the simpler fly It’s very difficult to get anything approaching causality because they’re are so many variables in gut bacteria populations. It’s a huge ecosystem unto itself.
Flies can eat literal garbage so I am also curious how their guts do not have arbitrary digestive problems (let's just say there's not much quality control on the input). Also whether they develop infections.
I think we're still far away from that, but we're trying to get there. Some successful work has been done based on AGORA models [1], where the simulations seem to roughly match the reality of simplified systems. For example, for a five-member community of bacteria, answering questions like "what happens if we remove bacteria B from the community?", but not too much beyond that yet.
Those are much, much simpler systems. Your average human microbiome has 30+ trillion cells in it, too say nothing of the intestinal cells. That's not getting into the underlying complexity of the cells themselves.
