The intestinal microbiome comprises a heterogeneous population of microbes that share space and resources with the host. Recent experimental and clinical findings suggest that in autoimmune disease, the composition of the gut microbiota is altered. We are now starting to elucidate the functional relevance of such changes. These changes have been associated in recent years with diseases such as Inflammatory Bowel Disease, Diabetes, Rheumatoid Arthritis, Multiple Sclerosis, and Asthma, among others.

Experimental models of autoimmunity are helping us to determine mechanistically the alterations in the complex intestinal communities in the endocrine, immune and neuronal system and the clinical implications of such changes. Efficacious treatments for most human autoimmune conditions are currently lacking. However, there is now accumulating evidence that the gut microbiome plays key roles in the regulation of tolerance mechanisms and that it may be a major environmental risk factor for autoimmune diseases. Accordingly, it is now hypothesized that intervention of the gut microbiome could result in novel therapeutic strategies to treat these diseases.

In this Research Topic, we aim to assemble a series of comprehensive Reviews, as well as novel findings, that explore the intestinal microbiome as a therapeutic target. We will strongly focus on worldwide research efforts based on dietary interventions, probiotic and prebiotic approaches for the prevention and treatment of autoimmune conditions such as Rheumatoid Arthritis, Diabetes, Inflammatory Bowel Diseases and Multiple Sclerosis. We welcome the submission of Review, Mini-Review and Original Research articles that cover, but are not limited to, the following topics:

1. The nutrition-gut microbiome physiology axis and autoimmune disease.
2. The developing microbiota gut/brain axis in mice and humans.
3. Personalization of the microbiome for therapeutic and preventative use.
4. The role of diet in autoimmune and inflammatory disorders.
5. Therapeutic use of probiotics and/or prebiotics for autoimmune disorders.

Keywords: Gut microbiota, Microbiome, Probiotic, Prebiotic, Autoimmune disease, Gut-brain axis

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.