Food‐grade antimicrobial ɛ‐polylysine transiently perturbs the structure of the murine gut microbiome

A scientific consensus has emerged that dietary components could guide the establishment and maintenance of microbial communities that colonize the distal gastrointestinal tract. Although ubiquitous in various food systems, it is unknown to what extent that antimicrobial compounds interact with endogenous gut microbiota once consumed. In this study, we investigated the influence of food‐grade biopolymers (i.e. ɛ‐polylysine, pectin, and ɛ‐polylysine‐pectin complexes) on the murine microbiota. Accordingly, CD‐1 mice were fed biopolymers incorporated into a high‐fat diet over a 9‐week time course. Microbial phylogenetic diversity present in fecal extracts were ascertained by high‐throughput amplicon sequencing of the 16s rRNA gene. Moreover, community function was predicted from relative abundances of taxa using PICRUSt. Interestingly, dietary ɛ‐polylysine transiently altered the gut microbiome prior to restoration of the initial microbial population structure at the end of the feeding trial. This is indicative of a community adaptive response to ɛ‐polylysine that is now known to be active against microbes in vivo . Moreover when the cationic ɛ‐polylysine is associated with the anionic polymer pectin, this micro‐bioactive perturbation is mitigated. Finally, the absolute population structure of these murine gut microbial communities was observed to be sex‐dependent, but did not alter the response trajectory to exogenous biopolymers. Support or Funding Information USDA