16S rRNA Metagenomic Profiling Reveals Diet-Induced Shifts in Gut Microbial Diversity and Taxonomic Structure in Guinea Pigs

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Abstract
Diet plays a pivotal role in shaping the gut microbiota, influencing host physiology, immune function, and nutrient metabolism. In this study, we evaluated the impact of three distinct feeding systems—Forage only, Balanced feed only, and Mixed system—on the cecal microbiota of guinea pigs (Cavia porcellus) using 16S rRNA gene amplicon sequencing in a randomized allocation of 18 males across the three diets (n = 6 per group) over 7 weeks. A total of 2,135,852 high-quality reads were obtained, with rarefaction curves and Good’s coverage confirming sufficient sequencing depth. Alpha diversity indices revealed significantly higher microbial richness and evenness in the mixed group, while beta diversity analyses demonstrated distinct microbial community structures across diets. Taxonomic profiling showed that forage-based diets enriched fiber-degrading genera such as Fibrobacter and Treponema, whereas the Balanced feed group favored mucin- and protein-degrading bacteria like Akkermansia and Bacteroides. LEfSe and t-test analyses identified several biomarkers and diet-specific genera, suggesting functional divergence in microbial metabolism. Forage-fed animals showed microbiota associated with short-chain fatty acid production and enhanced fiber utilization, while the Balanced feed group showed microbial traits linked to mucin degradation and potential gut barrier disruption. These findings highlight the strong influence of dietary composition on gut microbial ecology and suggest that fiber-rich diets promote a more diverse and functionally beneficial cecal microbiome in guinea pigs.

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