A series of complex physiological processes underlie the development of the microbiota, gut, and brain in early life, which together communicate via the microbiota-gut-brain axis to maintain health and homeostasis. Disruption of these processes can lead to dysbiosis of the microbiota, pathophysiology of the gut and behavioral deficits including depression, anxiety and cognitive deficits. Environmental exposures, particularly in early life, can interfere with development and impact these pathways. This review will focus on the role of the microbiome and the gut in neurodevelopment and neurodegeneration as well as the impacts of environmental exposures, particularly to the neurotoxicant polychlorinated biphenyls (PCBs), given that the gut serves as the primary exposure route. There exists extensive research on the importance of the microbiome in the developing brain and connections with autism spectrum disorder (ASD) and increasing links being established between the microbiome and development of Alzheimer's disease (AD) in the elderly. Finally, we will speculate on the mechanisms through which PCBs can induce dysbiosis and dysregulate physiology of the gut and brain.