Good Reddit comment on why science still has a long way to go in studying the microbiome:

The thing is that these bacteria are a big mystery. We know they're there and that they do something important - experimental data shows as much - but we don't know what they are exactly. We can't really plate these bacteria to expand them in culture because the microenvironment of the gut is obviously crucial to these bacteria and the usual glass + media environment of the plates we use for E. coli, for example, does not support them. Some or all species may also be highly sensitive to light (since they're in the darkness of our gut) and temperature (since they've always been at a warm 98.6 F). It's entirely possible and perhaps probable that they depend on our own biological processes to live. To isolate them, we'd essentially have to devise a culture method that mimics a human gut without any human gut to contaminate the experiment. Without plating, we can't really sequence their genome or understand the full spectrum of proteins involved in their life cycles.

They're attracting a lot of attention now because of data showing their role in disease (and thus medicine and financing) but it's also like exploring the ocean: it's a vast depth of undiscovered information that's been with us since long before humans even existed, but only now are we starting to be able to truly understand it. I suspect that once methods for examining the gut microbiome improve, our ability to treat a wide variety of diseases will explode with new therapies.

150 Reddit comments:

http://reddit.com/r/science/comments/2qokum/good_bacteria_in_gut_may_ease_anxiety_and/

From the live science article:

Recent studies in animals show that changes in the gut bacteria community appear to make mice less anxious, and also affect levels of the stress hormone cortisol.

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Scientists are now interested in studying whether probiotics (strains of good bacteria) or prebiotics (carbohydrates that serve as food for those bacteria) could be used to treat anxiety or depression, or if the substances improve patients' response to psychiatric drugs, said study author Philip Burnet, a researcher in the University of Oxford's department of psychiatry. [5 Ways Gut Bacteria Affect Your Health]

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Researchers aren't sure exactly how changes in gut bacteria might affect the brain. Some researchers suspect that the vagus nerve — which conveys sensory information from the gut to the brain — plays a role. Gut bacteria may also affect the immune system, which could, in turn, influence the brain, Burnet said.

More study is needed.