Gut Microbiota and Immunomodulatory Effects of Fruit Pomace: Mechanistic Insights and Critical Review of Metabolite-Mediated Pathways

Gut microbiota are vital components of the human gastrointestinal system, colonizing the gut from birth and existing in trillions, particularly in the colon. They contribute to host health through symbiotic interactions, nutrient metabolism, and production of bioactive metabolites, whereas disruptions in their composition may lead to dysbiosis. Recent studies indicate that fruits and fruit-derived extracts can significantly modulate gut microbiota, with important consequences for immune regulation and overall health. Fruit pomaces are valuable, sustainable resources because they are rich in bioactive compounds, phytochemicals, and nutrients that can influence gut microbial ecology, immune responses, and metabolic pathways. Their utilization also supports circular bioeconomy and sustainable waste management. This review summarizes evidence on interactions among fruit pomace components, gut microbiota, and immune cells, drawing on findings from metagenomics, metabolomics, and predictive modeling. Available evidence indicates that fruit pomaces can modulate microbial ecology in a substrate-, dose-, and host-dependent manner and affect potentially health-associated taxa. These shifts may be accompanied by changes in short-chain fatty acids, bile acid derivatives, tryptophan-derived indoles, and polyphenol catabolites. However, evidence strength varies across in vitro, animal, and human studies. Future work should prioritize standardization, multi-omics integration, and personalized nutrition.