Host–microbiome ecosystem

The host–microbiome ecosystem refers to the complex, symbiotic relationship between a host organism and the trillions of microorganisms—including bacteria, fungi, viruses, and archaea—that inhabit its body surfaces and cavities (PMC, 2023). This ecosystem is fundamental to host health, performing essential functions such as the maturation of the immune system, the synthesis of vitamins, and the fermentation of indigestible dietary fibers into bioactive metabolites like short-chain fatty acids (Frontiers in Immunology, 2024). Dysregulation of this intricate balance, a state known as dysbiosis, has been linked to the pathogenesis of numerous conditions, including inflammatory bowel disease (IBD), obesity, type 2 diabetes, and certain cancers (PMC, 2022). Therapeutic strategies targeting the ecosystem include the administration of probiotics, prebiotics, and live biotherapeutic products (LBPs), as well as fecal microbiota transplantation (FMT) to restore microbial diversity (Taylor & Francis, 2024). Furthermore, the microbiome acts as a virtual organ that can significantly alter the pharmacokinetics of conventional drugs through enzymatic biotransformation or bioaccumulation, thereby influencing treatment efficacy and toxicity (Gut, 2020). Understanding these interactions is central to the development of precision medicine approaches that leverage the microbiome to improve patient outcomes (PMC, 2024).

Other names

Human microbiomeMicrobiota-host axisCommensal floraHost-microbe immunological axisGut-microbiota-host axis

Modulation of microbial composition and diversity, restoration of commensal populations, production of bioactive metabolites (e.g., short-chain fatty acids), and competitive exclusion of pathogens.