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Impacts on both short and long-term health are severe in the case of deficiencies in micronutrients, such as vitamins and minerals. An important cause underlying these reduced bioavailability is probably reduced caloric intake and/or insufficiency in absorption in the gastrointestinal system. The gut microbiome is now apparently playing an important role recently seen from clinical and in vivo studies. In fact, the level of micronutrients can be regulated by commensal bacteria in interference with biosynthetic processes and through alteration of the absorption process. The study discusses the mechanisms by which gut microbiota affects absorption of vitamins and minerals, conversely, how these nutrients impact gut microbiome. It goes on to discuss the possibilities of using individualised microbiome-based therapies for shortages of micronutrients and general benefits for health.