That's my thinking as well. Depression leads to lifestyle changes which includes dietary changes which can cause certain bacteria to grow faster, as your gut bacterial makeup changes constantly based on what kind of food you consume and which microorganisms are specialized for it.

I think there will be some breakthroughs by studying the human microbiome, for example there could be reasons that a moderately harmful microorganism or strain becomes dominant in your gut for whatever reason and causes problems, but from my personal anecdotal experience with gut health and diet, I believe most issues will still be solved with dietary changes and perhaps some targeted antibiotics or antimicrobial treatments in general.

I'm also willing to bet we'll discover a lot of immune involvement in the regulation of various bacterial population in the gut. There must be an adaptive system that minimizes or eliminates most harmful organisms in the gut, otherwise we'd all be dead.