Description
Background/Objectives: 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. Methods: Mice were fed either a healthy AIN93G diet (AIN) or a total Western diet (TWD), with or without 2.6% (w/w) 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. Results: 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. Conclusions: 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.
Author ORCID Identifier
0000-0002-7993-0117
Document Type
Dataset
DCMI Type
Dataset
File Format
1. Benninghoff_Q2_mapping.csv provides the sample identification details including the sample site, time point, basal diet, and supplement group for each sample ID. 2. Benninghoff_Q2_ASV_counts.csv provides the 16S rRNA sequence count data for all samples for each amplicon sequence variant identified. 3. Benninghoff_Q2_taxonomy.csv provides the mapping of amplicon sequence variants to bacteria taxonomy. 4. Benninghoff_Q2_tree provides the phylogenetic tree file for the data set.
Publication Date
7-25-2025
Funder
USDA, National Institute of Food and Agriculture (NIFA)
Publisher
Utah State University
Award Number
2021-67018-33938
Award Title
Dynamics of the gut microbiome response to dietary intervention with anthocyanin-rich foods
Methodology
The experiment included the following experimental diets: AIN (American Institute of Nutrition AIN93G standard healthy diet); TWD, the total Western diet; the AIN+ 2.56% (w/w) CocoaVia™ Cardio Health powder; and the TWD + 2.56%% (w/w) CocoaVia™ Cardio Health powder. Mice were humanely euthanized and the cecal, fecal, and mucosal microbiomes were assessed by 16s rRNA sequencing prior to induction of colitis (pre-DSS), during active colitis (colitis), and 14 days later during recovery from gut injury (recovery). Sequencing data were processed via QIIME2 and DADA2. The DADA2 R package implements the full amplicon workflow (filtering, dereplication, chimera identification, merging paired end reads) and generates an amplicon sequence variant (ASV) table and representative sequences. To assign taxonomy, the QIIME feature-classifier classify-sklearn command was used with a classifier pre-trained for the V4 region, silva-138-99-515-806-nb-classifier.qza, and the most recent release of the Silva database (138 SSU)., and the resulting sequence count data are provided as ASV files in .csv format, with the corresponding taxonomy and mapping files also in .csv format.
Scientfic Names
Monoglobaceae, Eggerthellaceae
Language
eng
Code Lists
AIN, AIN93G diet
CP, cocoa polyphenols
CON, control
DSS, dextran sodium sulfate
Pre or Pre-DSS, prior to DSS treatment
COL, colitis
REC, recovery
TWD, total Western diet
Ce, cecal
Fe, fecal
Mu, mucosal
Disciplines
Dietetics and Clinical Nutrition | Digestive System Diseases
License
This work is licensed under a Creative Commons Attribution 4.0 License.
Recommended Citation
Benninghoff, Abby D., "Cocoa Polyphenols Modulate the Mouse Gut Microbiome in a Site-Specific Manner" (2025). Browse all Datasets. Paper 246.
https://digitalcommons.usu.edu/all_datasets/246