Going up a meta-level, for different types of research/analysis, its also important to ask "when is it important to look at gut/contents of gut as separate" and "when should we use a systems understanding".
My personal opinion is that modern medicine doesn't really like to think about the systems, because it's easier to look at something in isolation. Sometimes this is helpful - simply the problem space and you can simplify the solution - but much of the time it is inappropriate.
In tribal cultures, "medicine men" are both doctors and spiritual leaders. Historically in the Western world, doctors were some of the best educated people in town and some of the wisest people in town and everybody knew each other in a small town. The doctor made house calls with his little black bag.
Now doctors mostly don't make house calls because we use so much tech for diagnostics that you can't carry it with you. Star Trek's Dr. McCoy and his tricorder was modeled on the "little black bag" pattern of medicine and it married the idea of tech to that model and he could diagnose anything with the super advanced gadget in his hand while going to where the patient was. This is not how it has gone in real life.
In the process of making house calls, a doctor casually picked up a lot of information by observation that didn't require him to ask questions. He saw how clean your house was. He saw if you lived alone or with family. Etc.
Medicine has moved to a place where we treat people like specimens in a petri dish and as if their physical health is a separate question from the rest of their life. The reality is these are deeply intertwined and cannot be neatly separated.
The systems we need to be looking at are not just systems within the body but how the systems those bodies exist within impact the human body. And we aren't even really thinking in that direction yet.
My personal opinion is that modern medicine doesn't really like to think about the systems, because it's easier to look at something in isolation. Sometimes this is helpful - simply the problem space and you can simplify the solution - but much of the time it is inappropriate.