When research makes gut bacteria a suspect, they aren't taking about bacteria getting into the brain, but how that bacterial presence in the body impacts the brain through toxins absorbed into the bloodstream, poor absorption of nutrients, immune system function, etc, so if a mother has all this going on in her system, can we rule out the impact it has on her fetus? Not yet, I think.
The real issue here, I think, is more how a person with autism can manage their symptoms, and it's undeniable that promoting good gut bacteria and avoiding modern semi-dwarf strain wheat, A1dairy, gluten in general, and therapy have all had success in various people, although the effectiveness varies highly, from no effect at all to totally reversed, and everywhere in between.
Till research finds the smoking gun/guns and the direct treatment for each, we are left to trial and error in our own personal experiments.
_________________
We are not so different from potted plants in that, if given everything we need to be properly nourished, the outcome can be incredibly contrary to when we are not. A flower won't grow in flour, and neither can we.