Out of curiosity, did you get a microbiome test (e.g. from Viome) before and after removing each one of these elements from your diet, or did you make conclusions based on how you felt? Of course everyone is different, but I think published research supports your suggestion that sugar and alcohol are "bad" and fruits, vegetables, and resistant starch are "good", but disagrees on coffee. Here's a recent study showing association between high coffee intake and "good" gut microbiome [1]. I put good and bad in scare quotes because it seems the science around this is still pretty weak, mostly based on associations rather than clear and verified mechanisms.
[1] https://gi.org/media/press-info-scientific-meeting/featured-...
Sorry for the confusion. When I mentioned coffee I was referring to IBS symptoms, not microbiome. Caffeine increases digestive secretions and causes colonic motor activity. Even decaf coffee increases secretions. For a review, see:
If coffee is causing IBS symptoms (diarrhea), I would imagine that isn't good for your microbiome.
I haven't had any microbiome tests, and it's very difficult to robustly test for the effects of individual foods without doing a placebo controlled trial. However, after removing fizzy HFCS soda drinks, I seem to not have any symptoms that I would associate with an abnormal microbiome in the past year (smelly farts, followed by urgent need to poop, followed by large amount of soft poop after eating, during a period of long-term zero stress). I've made a number of other changes to my diet, such as not drinking tap water, but I suspect HFCS was the main culprit, as the scientific evidence strongly backs that up.
Stress is another main cause of IBS, due to its effects on gut motility.
