The human microbiome consists of bacteria, archaea, viruses, and eukaryotes that inhabit both the internal and external surfaces of the body. These microorganisms play a significant role in human physiology, influencing health and disease by enhancing or impairing metabolic and immune functions. Different microorganisms colonize various body sites, each adapting to the unique characteristics of its environment. Facultative anaerobes are more common in the gastrointestinal tract, while strict aerobes dominate areas like the respiratory tract, nasal cavity, and skin. The immune system and these indigenous microbes have evolved together, leading to a balanced biological interaction. Disruptions in the gut microbial community, often influenced by lifestyle or underlying diseases, contribute to various health issues. Such dysbiosis increases susceptibility to infections, which vary depending on the affected anatomical site. The diversity of the human microbiota is responsible for the specific metabolic functions at each body site. Thus, understanding the composition and activities of the human microbiome is crucial for insights into its role in health and disease.