Diluted vinegar; not a lot, not every meal, but a little bit once a day(I usually take it with canned seltzer water at dinnertime). It's the oldest recorded all-purpose tonic and it has a very clear purpose in digestive health by biasing the body's pH balance a little more acidic, which makes some foods easier to stomach, and also pushes the adaptive fitness of the gut.

While the scientific framework I'm building off of is patchy, I think of the gut biome as something you have to "train up" to give effective responses instead of dumping its issues onto other regulatory mechanisms, so exposing it to a variety of training scenarios would be an instrumental part of that, and it probably wouldn't be a factor of specific foods so much as general %s of fiber, fat, acidity, salinity, etc.