A shift in microbial populations in the gut has been associated with various neurological diseases and plays a role in the health of the mucosal immune system. By using next generation sequencing techniques, behavioral assays, and metabolomics we probe the complex relationships between the immune system and brain of the host and the gut microbiome to understand what it means to be healthy on a multi-organismal level. We hope these insights could pave the way for future novel therapeutics targeting involuted neurological disorders.