The microbiota–gut–brain (MGB) axis represents a dynamic, bidirectional communication network that links the central nervous system with the gastrointestinal tract and its resident microbiota. This axis plays a pivotal role in stress regulation, neurodevelopment, and immune programming, particularly during early life. Accumulating evidence from both animal and human studies suggests that alterations in gut microbial composition influence emotional and cognitive outcomes and that early-life adversity may program stress responsiveness through persistent microbiota dysbiosis. The first 1000 days—including gestation and the first 2 years of life—are critical for microbiota establishment and long-term health. Microbial metabolites—such as short-chain fatty acids, tryptophan derivatives, bile acid metabolites, and polyamines—act as neuroactive signaling molecules that influence brain function, neuroinflammation, and aging. Germ-free mouse studies and human trials further confirm the essential role of the microbiota in modulating brain activity and mental health. This chapter highlights recent advances in understanding the MGB axis and its implications for precision nutrition and sustainable strategies to promote cognitive resilience and healthy aging.