The microbiome is the collection of microbial organisms present in a given environment. The microbiome is generally characterized by the composition of bacteria, fungi, viruses, and archaea in a sample obtained from a specific source, ranging from human specimens to environmental collections.

Historically, microbiome research has included next-generation sequencing of the 16s rRNA gene to identify the bacterial community in a given sample. As technology has progressed and database curation has improved, a clearer picture of the human microbiome has emerged. More recently, characterization of the fungal community (i.e., the mycobiome) via sequencing of the ITS1/ITS2 region has also increased, along with characterization of the virome.

In relation to autism spectrum disorder, microbiome research has focused on the gastrointestinal (GI) tract. While there has been increasing interest in the microbiome, and more specifically the microbiome-gut-brain axis, there are still relatively few published research studies in clinical ASD populations. Within the current literature, there remain several limitations including the selection of appropriate control groups and adequate stratification based on GI symptoms. The high prevalence of GI symptoms and commonly employed dietary interventions (ex. gluten-free casein-free diet) and supplementation (ex. probiotics) further support the relevance of the microbiome in ASD.

Promising studies in animal models of ASD have provided compelling evidence of the role of the microbiome in ASD, with GI abnormalities (such as increased intestinal permeability and dysbiosis) manifesting alongside an ASD-like behavioral phenotype in both genetically and environmentally-driven mouse models. In addition, symptoms associated with ASD (both behavioral and GI) have shown significant improvement following microbial manipulation (ex. probiotics).

Larger microbiome studies with greater stratification based on GI, behavioral, and clinical phenotypes are emerging and underway. In addition, the first study showing the efficacy of microbiota transfer therapy (similar to fecal microbiota transplantation) in pediatric ASD was recently published, with the report of global improvements in both GI symptoms and core behavioral symptoms of ASD.

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