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Intestinal microbiota perform many functions that support human health. Deficiencies of essential minerals affect the growth of gut microbial community. The excessive supplementation of minerals can reduce the host ability to confront enteric infections by alternating intestinal integrity or improving pathogen capability. This article describes distinctive effects of the most important minerals on the human microbiome and explains the function of these minerals in relation to intestinal microflora activity. A better understanding of the mechanisms through which micronutrients change bacterial flora composition and promote health or disease conditions is needed to improve our knowledge of the causal relationship between the minerals and gut microbiota.