Engraftment of beneficial taxa and functional genes

Engraftment of beneficial taxa and functional genes refers to the successful colonization and persistence of exogenous microorganisms and their associated metabolic pathways within a host's microbiome following therapeutic intervention (Smillie et al., 2018, Cell Host & Microbe). This process is the primary objective of Live Biotherapeutic Products (LBPs) and Fecal Microbiota Transplantation (FMT), aiming to restore a healthy microbial ecosystem (FDA, 2022). Successful engraftment is characterized by an increase in microbial diversity and the re-establishment of key functional roles, such as the production of short-chain fatty acids or the conversion of primary to secondary bile acids (Buffie et al., 2015, Nature). In diseases like recurrent Clostridioides difficile infection, engraftment of commensal bacteria outcompetes the pathogen for niches and nutrients, thereby resolving the infection (Khanna et al., 2016, Mayo Clinic Proceedings). While not a single molecular target, it serves as a critical pharmacological endpoint for evaluating the efficacy of microbiome-targeted therapies like Vowst and Rebyota (FDA, 2023). Monitoring engraftment typically requires metagenomic sequencing to track donor-derived strains and functional gene profiles over time to ensure therapeutic durability.

Other names

Microbiome engraftmentMicrobial colonizationGut microbiota restorationFunctional gene restorationCommensal engraftment

Restoration of microbial diversity and metabolic functions, such as bile acid metabolism, to inhibit pathogen growth and modulate host immunity (Buffie et al., 2015, Nature; FDA, 2023).