Microbiota play a crucial role in human health and disease. The human microbiota, consisting of bacteria, fungi, viruses, and archaea, is found in various body sites, including the gut, oral cavity, respiratory tract, skin, and vagina. The microbiota contributes to homeostasis and immune regulation, but dysbiosis can lead to diseases such as cardiovascular diseases (CVDs), cancers, and respiratory diseases. This review discusses the current understanding of how microbiota links to host health and disease development. It covers the role of microbiota in healthy conditions, such as the gut-brain axis, colonization resistance, and immune modulation. It also highlights the pathogenesis of microbiota dysbiosis in disease development, including dysregulation of community composition, immune response modulation, and chronic inflammation. Finally, it introduces clinical approaches that utilize microbiota for disease treatment, such as microbiota modulation and fecal microbial transplantation. The human microbiota is composed of various bacterial phyla, including Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. The composition of microbiota varies by site, with the gut microbiota being the most significant in maintaining health. The gut microbiota plays roles in nutrient extraction, metabolism, and immunity. The oral microbiota is the second largest microbial community in the human body, and its composition varies across different habitats. The lung microbiota is also present, with its composition influenced by microbial immigration, elimination, and reproduction rates. The skin microbiota varies by geographic region and is influenced by physical and chemical differences. Microbiota in health includes the "healthy" gut microbiota, which is stable and symbiotic with the host. The gut microbiota is composed of bacteria, yeasts, and viruses, and a healthy microbiota community has high taxonomic diversity and stable core microbiota. The gut microbiota varies with age and environmental factors, and its composition differs in different parts of the gastrointestinal tract. The microbiota also differs by age, with diversity increasing from childhood to adulthood and decreasing in older age. Rodent models are used to study the pathogenic and therapeutic potential of microbiota in various diseases. The human and murine gut microbiota have significant differences in composition and abundance, particularly in the Firmicutes/Bacteroidetes ratio. Colonization resistance is a key function of microbiota, protecting against pathogenic infections. The gut microbiota contributes to colonization resistance through mechanisms such as nutrient competition, antimicrobial production, and bacteriophage deployment. The microbiota-gut-brain axis is a bidirectional interaction that influences neurophysiology and behavior. Gut microbiota can affect the brain through the gut-brain axis, with studies showing that microbiota can influence neurophysiology, behavior, and even neurodegenerative diseases such as Parkinson's disease. The gut microbiota also plays a role in the development of the immuneMicrobiota play a crucial role in human health and disease. The human microbiota, consisting of bacteria, fungi, viruses, and archaea, is found in various body sites, including the gut, oral cavity, respiratory tract, skin, and vagina. The microbiota contributes to homeostasis and immune regulation, but dysbiosis can lead to diseases such as cardiovascular diseases (CVDs), cancers, and respiratory diseases. This review discusses the current understanding of how microbiota links to host health and disease development. It covers the role of microbiota in healthy conditions, such as the gut-brain axis, colonization resistance, and immune modulation. It also highlights the pathogenesis of microbiota dysbiosis in disease development, including dysregulation of community composition, immune response modulation, and chronic inflammation. Finally, it introduces clinical approaches that utilize microbiota for disease treatment, such as microbiota modulation and fecal microbial transplantation. The human microbiota is composed of various bacterial phyla, including Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. The composition of microbiota varies by site, with the gut microbiota being the most significant in maintaining health. The gut microbiota plays roles in nutrient extraction, metabolism, and immunity. The oral microbiota is the second largest microbial community in the human body, and its composition varies across different habitats. The lung microbiota is also present, with its composition influenced by microbial immigration, elimination, and reproduction rates. The skin microbiota varies by geographic region and is influenced by physical and chemical differences. Microbiota in health includes the "healthy" gut microbiota, which is stable and symbiotic with the host. The gut microbiota is composed of bacteria, yeasts, and viruses, and a healthy microbiota community has high taxonomic diversity and stable core microbiota. The gut microbiota varies with age and environmental factors, and its composition differs in different parts of the gastrointestinal tract. The microbiota also differs by age, with diversity increasing from childhood to adulthood and decreasing in older age. Rodent models are used to study the pathogenic and therapeutic potential of microbiota in various diseases. The human and murine gut microbiota have significant differences in composition and abundance, particularly in the Firmicutes/Bacteroidetes ratio. Colonization resistance is a key function of microbiota, protecting against pathogenic infections. The gut microbiota contributes to colonization resistance through mechanisms such as nutrient competition, antimicrobial production, and bacteriophage deployment. The microbiota-gut-brain axis is a bidirectional interaction that influences neurophysiology and behavior. Gut microbiota can affect the brain through the gut-brain axis, with studies showing that microbiota can influence neurophysiology, behavior, and even neurodegenerative diseases such as Parkinson's disease. The gut microbiota also plays a role in the development of the immune