Influence of Eating Behavior and Dietary Patterns on Gut Microbiota Formation in Children with Autism Spectrum Disorder

Background/Objectives: Autism spectrum disorder (ASD) is often associated with gastrointestinal dysfunction and gut microbiota alterations. This study aimed to characterize the gut microbiota in children with ASD in relation to nutritional factors and to evaluate the effects of dietary interventions combined with probiotics. Methods: The study included 96 children with ASD and 39 neurotypical controls. Follow-up data after intervention were available for 60 children with ASD. Gut microbiota composition was assessed by 16S rRNA sequencing, and fecal calprotectin and zonulin were measured before and after intervention. Most children with ASD (n = 91) received a rotational or elimination diet for six months, and all participants with ASD received probiotics for 1.5 months. Results: Children with ASD showed significant microbiota changes compared with controls, including increased Prevotella, Sarcina, NK4A214 group, and RF39 taxon, along with reduced butyrate-producing bacteria, such as Roseburia, Eubacterium xylanophilum group, and Eubacterium ventriosum group. Formula feeding was associated with increased Odoribacter, whereas food selectivity was linked to higher Prevotella, Sarcina, Methanobrevibacter, and RF39. A rotational diet increased Erysipelotrichaceae UCG-003 and Streptococcus, while an elimination diet increased Butyricicoccus and reduced fecal calprotectin (p = 0.023). Fecal zonulin decreased significantly after intervention in the follow-up ASD subgroup (p = 0.018). Conclusions: The obtained data suggest that children with ASD may exhibit certain microbiota features associated with nutritional patterns. Dietary interventions combined with probiotics appear to be associated with microbiota modulation and a tendency toward improvement in markers of intestinal inflammation and barrier function.