Close interaction between gut microbiota, diet and health has long been recognized and is intensively studied. Recent research shows that microbiota signatures may serve as important biomarker in personalized nutrition allowing for a noninvasive yet highly efficient therapy of chronic diseases. Probiotics’ research brings the first human trial with next generation probiotic – Akkermansia muciniphila and demonstrates its safety and great potential for the treatment of metabolic disorders, but also shows that sequential application following a defined administration protocol, might be of particular relevance for therapy success. Plant-based dietary choices enrich gut microbial diversity, while recent studies show that spices, berries and nuts, known as nutritionally rich foods, appear to have prebiotic effects. Veganism and restricted feeding, which are recognized as promising approaches for combating obesity and related disorders are conferring their beneficial effect, at least partially, through microbiota modification.