Colonic Dysbiosis Is Associated with Gastrointestinal Disorders More than Mother–Child Epidemiological Traits in Mexican Children with Autism Spectrum Disorders

Introduction: Functional gastrointestinal disorders (FGIDs) are common comorbidities that affect the life quality of children with autism. Objective: This study investigated the link between clinical history and specific colonic fecal microbiota (CFM) markers with the pathophysiology of FGIDs in young children with autism patients. Methods: Thirty-nine young patients (2 and 18 years) were included in the study of FGIDs (+) cases (n = 18) and FGIDs (-) (n = 21) controls. Gastrointestinal disorders were diagnosed by standardized clinical tools (ROMA-IV and six-item gastrointestinal severity index), while bacterial markers, including Bacteroidetes, Firmicutes, Actinomycetes (Phyla); Lactobacillales, Clostridiales, Bifidobacteriales (Orders); B. fragilis, F. prausnitzii, B. longum, D. vulgaris and A. muciniphila (Species), were detected by targeting 16S rRNA and two-step PCR protocol. Results: The overall prevalence of FGIDs was significantly (p < 0.05) associated with cesarean delivery, the duration of milk formula consumption, and the presence of early intestinal symptoms during infancy. Furthermore, Bacteroidetes, Lactobacillales, B. longum, D. vulgaris, and A. muciniphila concentrations were significantly (p ≤ 0.03) higher in stool of patients with moderate symptoms, compared to those who were asymptomatic. Conclusions: Our results suggest that the CFM composition is a potential physiological predictor of FGID pathophysiology in a severity-dependent way in children with autism.