I read the article a couple of days ago and agree with your assessment that much more research is needed. I can see a lot of variables affecting the outcome of the sampling. Picky eater children won't have the same gut flora as children who eat a range of different foods, and many autistic kids are very picky about their diets. Many autistic children I've been around put things in their mouths like twigs, sticks, rocks, pieces of plastic, etc. that could easily introduce fungi, bacteria and viruses to their stomachs that other children aren't exposed to because they rarely, if ever, put those things in their mouths. It's unclear to me whether the mothers' gut flora is a contributing cause to autism in their offspring.
Thanks for posting.