Many children with autism spectrum disorders (ASDs) suffer from gastrointestinal 
problems such as diarrhoea, constipation and abdominal pain. This has stimulated 
investigations into possible abnormalities of intestinal microbiota in autistic 
patients. Therefore, we designed this study to identify differences (and/or 
similarities) in the microbiota of children with autism (without 
gastrointestinal dysfunction: n = 23; with gastrointestinal dysfunction: n = 28) 
and their neurotypical siblings (n = 53) who share a similar environment using 
bacterial tag-encoded FLX amplicon pyrosequencing. Regardless of the diagnosis 
and sociodemographic characteristics, overall, Firmicutes (70%), Bacteroidetes 
(20%) and Proteobacteria (4%) were the most dominant phyla in samples. Results 
did not indicate clinically meaningful differences between groups. The data do 
not support the hypothesis that the gastrointestinal microbiota of children with 
ASD plays a role in the symptomatology of ASD. Other explanations for the 
gastrointestinal dysfunction in this population should be considered including 
elevated anxiety and self-restricted diets.