Knowledge surrounding the trillions of microbes that inhabit the human gut has bloomed exponentially in recent years, and the emerging concept of a gut-brain axis represents a major shift in how we think about neurological health. A recent workshop at the University of British Columbia, Canada brought together multi-disciplinary leaders in the field of microbiomics and brain health and aimed to serve as a springboard for future combined endeavors in these areas. This article provides the motivation for, and overview of, the workshop, and the next steps in establishing a cross-disciplinary initiative on Brain Health and the Microbiome.