Cocoa Polyphenols Modulate the Mouse Gut Microbiome in a Site-Specific Manner

<b>Background/Objectives:</b> The dietary modulation of the gut microbiome is a promising strategy for mitigating gastrointestinal diseases, such as inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CAC). Cocoa powder is rich in polyphenols, including (-)-epicatechin and (+)-catechin, which have been associated with beneficial effects on gut health and microbiome modulation. Importantly, changes in the bacterial populations associated with the gut mucosal layer may have different health impacts compared to changes in cecal or fecal microbiomes. This study investigated the effects of cocoa polyphenol supplementation on microbiome composition across the cecal, fecal, and mucosal compartments in a mouse model of colitis. <b>Methods:</b> Mice were fed either a healthy AIN93G diet (AIN) or a total Western diet (TWD), with or without 2.6% (<i>w</i>/<i>w</i>) CocoaVia™ Cardio Health Powder. Gut microbiomes from the cecum, feces, and colon mucosa were profiled using 16S rRNA sequencing at three time points: pre-, during, and post-colitis. <b>Results:</b> Microbiome composition varied substantially by site, with reduced richness and distinct taxa in the mucosal layer compared to cecal and fecal communities. The TWD significantly altered microbial composition, decreasing species evenness and shifting beta diversity. Cocoa polyphenol supplementation modulated microbial communities in a site-specific manner, increasing diversity and promoting rare taxa (e.g., Monoglobaceae, Eggerthellaceae, and RF39) primarily in cecal and fecal samples. Mucosa-associated communities were less responsive. <b>Conclusions:</b> These findings underscore the importance of the sampling site in gut microbiome research. Cocoa polyphenols exert site-selective effects, particularly in the gut lumen, highlighting the importance of considering anatomical context in dietary intervention studies aimed at improving gastrointestinal health.