I find the theory highly plausible, that a disruption of the gut flora, could have repercussions for brain development, cognitive changes, mental disorders.
I've read certain pathogens are implicated, suspected to play a role in Parkinson's, and Alzheimer's.
It's not inconceivable a gut-brain axis connection, as it's been widely reported for decades now, with the higher incidence of gastrointestinal problems associated with Autism. Particularity gluten, wheat sensitivity, akin to Caelic disease.
I'm sure you've heard the stories about people going grain free, and claiming cognitive effects, less autistic behavior, from a simple dietary change. This Theory would seem to back that up. As What you eat, affects microbiome, changes the balance, ratios of specific strains.