Intestinal microbiome ecosystem and associated host pathways (Gut microbiome)

The intestinal microbiome ecosystem refers to the complex community of trillions of microorganisms, including bacteria, fungi, viruses, and archaea, that reside in the human gastrointestinal tract and interact with host pathways (NIH, 2023). This ecosystem plays a fundamental role in human health by aiding in the digestion of complex carbohydrates, synthesizing essential vitamins, and training the host immune system to distinguish between commensal and pathogenic organisms (Nature Reviews Gastroenterology & Hepatology, 2022). It communicates with distant organs through the production of metabolites like short-chain fatty acids (SCFAs), which influence host metabolic and neurological functions via the gut-brain axis (Cell, 2021). Dysbiosis, or a functional imbalance in this ecosystem, is strongly associated with various pathologies, ranging from localized gastrointestinal infections like Clostridioides difficile to systemic conditions such as obesity and autoimmune diseases (PubMed, 2023). Therapeutic strategies targeting this system include the use of antibiotics to eliminate pathogens, prebiotics and probiotics to encourage beneficial growth, and fecal microbiota transplantation (FMT) or defined microbial consortia to restore a healthy ecological state (FDA, 2023). As a therapeutic target, the microbiome represents a shift from traditional single-molecule pharmacology toward ecological and systems-based medicine.

Other names

Gut microbiotaIntestinal floraHuman intestinal microbiomeGut-host axisGastrointestinal microbiome

Modulation of microbial composition to restore ecological diversity, competitive exclusion of pathogenic species, and regulation of host physiological signaling through the production of microbial metabolites such as short-chain fatty acids (SCFAs) and secondary bile acids (Nature Reviews Microbiology, 2022; FDA, 2023).