"One of them, Morganella, was significantly increased in a microbial survey of the 181 people in the study who _later_ developed depression."

they would have been diagnosed with depression first leading to increase in morganella, if it was the other way around? agree this could be correlation, but I guess thats why they say that the field is still in its infancy.

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.

Do they claim causation anywhere? All I see is them saying there appears to be a link.

Yes.It establishes linking, and claim further evidences of "causation".

"seems to be “further proof" that inflammation caused by gut microbes can influence mood, Gilbert says."

That appears to be a quote from another microbiologist who wasn't involved with the study. Even he only says it "seems to be" rather than "it is".