Microbiota plays an important role in multiple physiological functions such as immunity and nutrient absorption and creates a complicated relationship with the host. However, increasing evidence has revealed that changes in microbiota composition and its derived metabolites have pivotal effects on the pathogenesis of different disorders including endocrine diseases. In addition, findings from a large number of documents have shown that host microbiota is a contributor to patients’ response to therapies. In this chapter of the book, we first discussed the interaction between microbiota and different host organs. Then, the dysbiosis present in multiple metabolic disorders is investigated along with how it can affect the host’s metabolic pathways and disturb their homeostasis. Moreover, we provided information on utilizing microbiota characteristics as biomarkers of different diseases in order to help diagnose or predict a specific condition and introduced multiple supplementations and strategies to manipulate the composition of gut microbiota toward increasing beneficial microorganisms and restoring a healthy composition. Finally, we discussed omics studies and the comprehensive information they provide regarding individual microbiota to shed light on their potential usage in precision medicine.