•The intestinal microbiota regulates metabolic, inflammatory, immune and neurobiological processes.•The microbiota can be modulated qualitatively and quantitatively, and nutrition is the most important factor.•Probiotics can produce short-chain fatty acids, neurotransmitters, antioxidants and vitamins.•There is growing scientific evidence about the phenotypic effects of prebiotics, probiotics and postbiotics on physiology.•Microbiota-based precision nutrition is a promising tool in health and physiological performance.