The past decade has witnessed a paradigm shift in brain research. A transition from a dogmatic brain-focused approach toward a holistic conception of health that integrates key signaling hubs of the human body—such as the gut and its microbial populations, the peripheral immune system, and other mucosal barrier surfaces—is increasingly acknowledged as necessary to understand and cure neurological disorders, such as Alzheimer’s disease, stroke and brain tumors. We investigate the physiological connections between the digestive, immune and nervous systems in a holistic approach, allowing better understanding of neurological diseases in the context of aging. We study how processes which take place in the gut, affect brain functions in health and disease, and looking at the whole-organism level to identify novel targets to treat brain pathologies.