Recent advances in targeted manipulation of the gut microbiome by prebiotics: from taxonomic composition to metabolic function

Diet-related diseases are characterized by ‘dysbiotic’ gut microbiomes that represent a promising therapeutic target. Microbiome-based therapies broadly modulate the composition and function of gut microbiomes, but exhibit inconsistency due to wide individual variability between patients. Alternatively, personalized microbiome-targeted nutrition therapies are rapidly developing under increasing interest. In light of the recently renewed interest in harnessing fibers and polyphenols for the targeted manipulation of gut microbial community structure and metabolic output, we propose the term ‘targeted prebiotics’ to denote microbiota-directed fiber with a discrete structure, and discuss recent advances in targeted manipulation of health-promoting microbes by current and candidate prebiotics. We further explore the application of targeted prebiotics in personalized nutrition, aiming for predictable shifts in bacterial composition, functional genes, and metabolites. In conclusion, our review will advance the precise modulation of the gut microbiome via the optimization of prebiotic-based strategies.