Microbiota is a complex and diverse collection of microorganisms, including bacteria, viruses, yeast, and fungi, that colonize various parts of the human body, such as the skin surface, oral cavity, intestine, and genital tract. These microorganisms are essential to maintaining a healthy immune system, digesting food, and producing essential vitamins and hormones. They also play a critical role in protecting against harmful pathogens and diseases by competing for resources and producing antimicrobial substances. In short, the microbiota is an integral part of our body’s ecology and is crucial for our overall health and well-being. Depending on their location, microbiota can be categorized as gut, oral, respiratory, or skin microbiota. The imbalances or dysbiosis in the microbial communities can lead to disruptions in various bodily processes and procedures, potentially contributing to diseases. This chapter discusses the current perception of how microbiota impacts health and disease pathogenesis from the perspective of microbial community composition and interactions with the human host and its immune system. Finally, we discussed some clinical approaches that leverage microbiota for treating diseases, such as modulating the microbiota in probiotic and prebiotic approaches or using fecal microbiota transplantation to restore microbial balance.