Host gastrointestinal microbiome ecosystem (Gut microbiome)

The host gastrointestinal microbiome ecosystem is a complex community of trillions of microorganisms, including bacteria, fungi, viruses, and archaea, residing in the digestive tract [NIH, 2012]. It functions as a virtual organ that plays a critical role in human health by aiding digestion, synthesizing essential vitamins like K and B12, and training the host immune system to distinguish between commensal and pathogenic organisms [Nature Reviews Microbiology, 2020]. Dysbiosis, or an imbalance in this ecosystem, is linked to a wide range of conditions, including Clostridioides difficile infection, inflammatory bowel disease, and metabolic disorders [PubMed, 2019]. Therapeutic strategies targeting the microbiome range from broad-spectrum antibiotics to fecal microbiota transplants (FMT) and live biotherapeutic products like Rebyota and Vowst, which aim to restore ecological stability [FDA, 2022; FDA, 2023]. As our understanding of the gut-brain and gut-lung axes grows, the microbiome is increasingly viewed as a central hub for systemic health and a high-priority target for novel biotherapeutics [Science, 2021]. The ecosystem is unique as a target because it involves modulating a dynamic community of living organisms rather than a single molecular pathway.

Other names

Gut microbiotaIntestinal microbiomeGastrointestinal floraHuman gut microbiomeIntestinal microbiota

Therapeutic interventions target the ecosystem to restore microbial diversity and ecological balance (eubiosis). This is achieved through the competitive exclusion of pathogens, the restoration of secondary bile acid metabolism, and the modulation of host immune and metabolic pathways via microbial-derived metabolites such as short-chain fatty acids [Nature Reviews Microbiology, 2020; FDA, 2022].