The growing trend recognising that gut bacteria affect all other body systems, the brain, of course, included, is often accompanied by what I think is a faulty assumption. That assumption is that there are healthy strains of bacteria that are difficult to cultivate that we should specifically insert into the gut (through pills, yogurt, or transplants, for example) and then keep alive by feeding with high fiber plants in order to maintain health.
The main reason I find this implausible is that it's not evolutionarily supported. There is just no strong evidence that evolving humans ate fibrous plants with any regularity. Moreover, any gut bacteria that we can't easily keep living inside us seem unlikely to have evolved there. It makes no sense that regularly eating something we didn't evolve to eat regularly, to keep alive something that doesn't appear to have evolved a strong penchant to stay alive in us, would be the only, let alone best way to maintain an inner environment conducive to health.
There do seem to be positive effects from taking probiotics, but I question the interpretation of that. One hypothesis I have is that the main benefit of probiotics is that they in turn displace worse strains of bacteria. If this is correct, then another, possibly better solution may be to minimise the worse bacteria by not feeding them. One way to not feed them would be to avoid fibrous plants.
(Please see my related post on germ-free mice, where I show that mice with no gut bacteria, contrary to common interpretation, are healthier than those with bacteria.)
Another possible explanation, is that these bacteria we are pushing mainly help people digest fibrous plants. So in people who eat fibrous plants, it is better to work to maintain these bacteria, than not to. However, this, too has the obvious alternative solution.
Antibiotics and the brain
I just learned about the potential benefits of antibiotics in autism. The author of the linked article has found evidence that negative symptoms of autism may be mitigated by taking antibiotics. His own son, for example, had improved eye contact, speech, energy, and motor control. This prompted him to look for clinical evidence, and he did find some preliminary such.
Often researchers suppose that such properties of antibiotics are coincidental, and unrelated to the antibiotic effects. For example, minocycline, the antibiotic used in the latter study, has been shown to have antioxidant properties that are neuroprotective. The mechanism is unknown, and I am not aware of people testing the hypothesis that the antioxidant property is a downstream effect of bacterial modulation.
I did find one nice exception to this. Antibiotics are known to improve cognition in hepatic encephalopathy. In this study, the researchers tried to discover a plausible mechanism for that. What they found was that there was a shift in the activity of different gut bacteria, resulting in an increase of many types of fatty acids in the blood. They speculated that these fatty acids, which brains like to use, were reponsible for the cognitive improvements.
Antibiotics often get a bad rap, because some conditions appear to get worse after you take them. People explain this with the story that after you've taken them, your gut is now prey to the "bad" bacteria, which for some reason never explained, naturally takes over in place of the "good" bacteria that "should" be there. This all appears rather backwards to me. I would think that if we were feeding our guts naturally, we wouldn't have to go out of our way to ensure this didn't happen.
What is salient to me is that supressing our gut bacteria, or changing the way they function from the default, is often having a positive effect that goes away when we go back to our normal way of treating those bacteria -- feeding them our Western diets. The common wisdom for dealing with that is to force in bacteria optimised for an onslaught of plant fiber. One wonders what would happen if instead, we just stopped the onslaught.