I changed the original title from "No, Autism Is Not Caused By The Gut Microbiome", because neither to article nor the study it criticizes are about what causes autism, but about a potential technique to diagnose it.
"children with autism tend to be finicky eaters..."
I haven't read the research but this sentence from the article suggests that there may be a relation to the microbiome. Because what we eat is controlled by microbiome. We crave sugar because organisms in the gut that feed on sugar are hungry. But I agree that the composition of the microbiome changes all the time and it's hard to draw conclusions.
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