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The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey ( Prevotella spp. , Bacteroides, Fusicatenibacter , and others) and gluten and dairy-free diets ( Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms., Importance: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD., Competing Interests: J.P., D.N., S.J., T.M., S.D., K.B., and S.T. are employed by Sun Genomics Inc. D.C.C. was co-supported by Sun Genomics Inc. J.A. and R.K.-B. are co-founders of Gut-Brain Axis Therapeutics Inc., which is developing microbiome-based treatments for autism and other disorders.

Irritable bowel syndrome (IBS) is characterized by abdominal discomfort and irregular bowel movements and stool consistency. As such, the gut microbiome has been posited as being influential for the syndrome. However, identifying microbial features associated with IBS symptom heterogeneity is difficult without large cohorts. Our aim was to identify microbial features associated with IBS and IBS subtypes compared to healthy controls and to determine if a synbiotic supplementation intervention could decrease the proportion of those microbial features. Stool samples from 490 individuals with IBS (including all dominant subtypes) and 122 individuals without IBS were analyzed with metagenomic sequencing. One hundred thirty-four IBS subjects were followed over time while receiving daily synbiotic supplementation, the composition of which varied between participants. IBS participants had significantly lower alpha diversity, an enrichment in Gram-negative bacteria, and a reduction in pathways associated with short-chain fatty acid and vitamin synthesis. Shigella species were significantly associated with IBS, while Eubacterium rectale and Faecalibacterium prausnitzii were associated with healthy controls. Random forest identified unique and overlapping microbial features associated with each IBS subtype. Longitudinal assessment of 134 IBS subjects receiving synbiotic supplements demonstrated a significant difference in microbial features and an increase in probiotic abundance across time. We identified microbial features that differentiate healthy and IBS subtypes. Synbiotic supplementation in IBS subjects did not result in alpha diversity change in the microbiome but did demonstrate changes in microbial features. Future work is needed to determine if the observed microbiome changes are associated with IBS symptom improvement. IMPORTANCE An estimated 35 million people in the United States and 11.5% of the population globally are affected by IBS. Immunity, genetics, environment, diet, small intestinal bacterial overgrowth (SIBO), and the gut microbiome are all factors that contribute to the onset or triggers of IBS. With strong supporting evidence that the gut microbiome may influence symptoms associated with IBS, elucidating the important microbes that contribute to the symptoms and severity is important to make decisions for targeted treatment. As probiotics have become more common in treating IBS symptoms, identifying effective probiotics may help inform future studies and treatment.