Effect of Probiotic Supplementation on Gut Microbiota in Children with Autism: A Pilot Randomised Controlled Trial

Background: Dysbiosis of the gut microbiota is common in children with autism spectrum disorder (ASD). Probiotics have the potential to improve outcomes in ASD by modulating the gut microbiota–brain axis. Methods: In a pilot randomised trial, children (2 to 5 years) with confirmed ASD (DSM-5 criteria) received either a multi-strain probiotic (450 billion CFU twice daily for one month, followed by once daily for three months) or placebo supplementation. Faecal microbiota profiles were assessed using pre- and post-supplementation samples. The primary outcome involved changes in gut microbiota diversity. Secondary outcomes included faecal short-chain fatty acid levels and behavioural changes. Results: Difficulties in recruitment and loss to follow-up for reasons including COVID-19 resulted in the enrolment of only 23 (probiotic: 9; placebo: 14) instead of the planned 40 children. There was no evidence of changes in the gut microbiota in probiotic-supplemented children. The common phyla were Bacillota_A (~50%), Bacteroidota (~18%) and Actinobacteriota (~10%). Alpha- and Beta-diversity showed no significant difference between pre- vs. post-supplementation samples. Bifodobacteriaceae increased significantly in the probiotic-supplemented group (p = 0.046). Conclusions: The increase in faecal Bifodobacteriaceae supports an evaluation of probiotics in ASD. Addressing the reasons for loss to follow-up is important when designing trials in this field.