OBJECTIVE: To provide an update of the advantages of new-generation molecular diagnostics to study the diversity of intestinal microflora and to evaluate its alteration in human diseases. METHODS: We review recent advances in understanding the complex ecosystem of gut microbiota based on a dynamic and mutual interaction with the host. RESULTS: In vaginal delivery, the contact with the mother's vaginal and intestinal flora is an important source of Lactobacillus, Prevotella and other Bifidobacterium. On the opposite, in cesarean delivery, direct contact of the mouth of the newborn with vaginal and intestinal microbiota is replaced by exogenous non-maternally derived bacteria colonizing the infants' intestine producing a less diverse flora. The original microbiome settings evolve during the growth converging to three main clusters defined "enterotypes" in the adult age. CONCLUSIONS: The key role in human health could depend on the balance between beneficial and harmful microbial species populating the gut, therefore the intestinal microflora can been considered as a potential biomarker and/or therapeutic target in intestinal and extra-intestinal diseases.
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