The main modern tools and techniques of epigenetic, dietary and biomicrobiotic protection of healthy ageing have been studied. Artificial intelligence, brain-microbiota neural networks allow to control interaction of genetic and epigenetic programs of ageing and healthy longevity. The new managed healthy biomicrobiota and personalized functional and balanced nutrition of ‘brain and microbiota’ is a long-term medical program of the patient, which allows the combined application of nutritional epigenetics and pharmacepigenetics, and the main thing to carry out prevention of polypragmasia. Multimodal tools, biochyping, neural and brain chips, next-generation (new) sequencing technologies create biomarkers to manage the structure of healthy biomicrobiota and functional nutrition, depending on the targets achieved. A functional food product using biomarkers and artificial intelligence technologies is a target breeding ground for both the body in general and biomicrobiota in particular. Chronomedical technologies are mathematical models and artificial intelligence that predict human biological age using DNA methylation data, histone modifications, nucleosome remodeling, and microRNA, and are the most accurate biomarkers of the aging process. Epigenetic mechanisms (DNA methylation, histone modifications, ncRNAs) are interconnected and form an ‘epigenetic network’. Lifestyle factors and environmental exposures leave epigenetic marks on our DNA that impact gene expression; some have protective effects while others are harmful. Genetic and epigenetic factors that ensure longevity and super-longevity require a reasonable new human interaction with nature and society, and responsibility for future healthy generations.