Gastrointestinal (GI) disturbances are commonly reported in children with autism, complicate clinical management and may contribute to behavioral impairment. Evidence of inflammation and anecdotal reports of improvement in some children following dietary modification, antibiotics and probiotics led us to profile host gene expression and to survey the microbiome in intestinal biopsies of children with autism and GI disturbances (AUT-GI) compared to children with normal neurological development and GI disturbances The intestine must maximize nutritional uptake of dietary components while maintaining a barrier to toxins and infectious agents. Dysregulation of intestinal homeostasis can have a profound impact on the gastrointestinal system, but can also manifest peripherally and influence overall human health. The investigatorsâ€™ previous research identified deficiencies in gene pathways involved in carbohydrate digestion in addition to changes in intestinal bacteria in biopsies from children with autism and GI disturbances. This project aims to investigate the extent to which other microbes, such as fungi and viruses, or other gene pathways, such those involved in inflammation, are associated with GI disturbances in autism. The findings promise to enhance our understanding of gene-environment interactions in autistic children with GI disturbances and provide a scientific foundation for rigorously assessing the utility of exclusion diets, antibiotics and probiotics in these children.