Michelle,

They're more linked than you might think, and a lot of good researchers are cognizant of the link; studies like the one Sam detailed here do not detract from the understanding that depression is triggered by environmental causes. Although when the research gets explained outside of the academic circles where it's conducted, many researchers fail to explain that -- which is a major problem because it gives readers the idea that the biological and environmental explanations are opposed.

What we do know is that environmental stressors (and especially specific types like shame and social defeat) trigger the same set of system-wide immunological responses that we see in response to sickness and physical wounds. Inflammatory responses are a natural part of this -- but inflammatory responses also appear to be linked to depression.

In fact some researchers have observed that the behaviors associated with depression appear to be similar to the overt behaviors we associate with sickness and wound recovery.

The true position of a gut biome study like Sam covered here is as a possible way of ameliorating the general inflammatory response. If it worked particularly well it might help alleviate depression from mystery causes but also might help reduce the intensity of depressive responses to external, identifiable causes.

At the same time, most of the research psychologists I know would agree that the physiological angle, alone, is not sufficient without addressing the identifiable outside causes of depression.