The symbiotic relationship with the microbial flora inhabiting our bodies plays an immense role in maintaining our vitality. The microbiota protects us from pathogens, hardwires our immunity, and engages in the production of essential micronutrient components. The human microbiota encompasses several thousands of fungi, eubacteria, archaea and viruses, with eubacterial cells alone totaling over 10 trillion and outnumbering our body cells 100 to 1. Next generation sequencing has allowed researchers to comprehensively assess the diversity of microbial species in the human microbiota and to estimate their proportions with stunning accuracy. This has led to a breakthrough in our understanding of associations between human health and the microbiota. This review focuses on the current state of research on key microbial communities inhabiting the human body: those of the gastrointestinal and genitourinary systems. Less studied microbial communities colonizing the nose, nasopharynx, auditory canal, eye, and skin, as well as some others, are not included in the review.