Interaction of Gut Microbiota and Food Bioactive Compounds

Dear Colleagues,

The human gut microbiome represents a complex molecular ecosystem where intricate biochemical interactions between microbial enzymes and dietary bioactive compounds fundamentally influence host health at the molecular level. This Special Issue aims to explore the molecular mechanisms underlying the bidirectional relationship between gut microbiota and food bioactive compounds, with particular emphasis on the gene expression profiles, protein interactions, metabolomic signatures, and signaling pathways that govern these processes. Recent advances in molecular microbiome research have revealed that bioactive compounds from various food sources—including polyphenols, prebiotics, probiotics, phytochemicals, and functional food ingredients—can significantly modulate gut microbial gene expression, enzyme activity, and metabolite production through well-defined molecular pathways. Conversely, gut microorganisms employ specific enzymatic machinery and metabolic networks to biotransform these compounds, generating novel metabolites with distinct molecular properties that affect bioavailability and biological activity in host tissues. This Special Issue welcomes original research articles, comprehensive reviews, and meta-analyses that investigate molecular-level interactions through the following:

• Molecular mechanisms of microbiota-bioactive compound interactions, including transcriptomic and proteomic analyses of microbial responses to dietary compounds;
• Enzymatic pathways and metabolic networks involved in microbial biotransformation of food bioactives, with detailed characterization of key enzymes and intermediates;
• Host–microbe molecular signaling cascades triggered by bioactive compound–microbiota interactions, including inflammatory pathways, metabolic regulation, and epigenetic modifications;
• The metabolomic and lipidomic profiling of gut microbial communities and host tissues following exposure to specific food bioactives;
• Molecular markers for personalized nutrition approaches based on individual microbiome genetic profiles and metabolic signatures;
• Structure–function relationships of bioactive compounds and their microbial-derived metabolites at the molecular level;
• Advanced analytical and computational methods for studying molecular interactions, including multi-omics integration, molecular dynamics simulations, and systems biology approaches.

We particularly encourage submissions that employ cutting-edge molecular techniques such as single-cell RNA sequencing, CRISPR-based functional studies, isotope labeling experiments, and high-resolution mass spectrometry to elucidate the precise molecular mechanisms governing these interactions. Studies should provide molecular evidence through gene expression analyses, protein quantification, metabolite identification, or pathway mapping to advance our understanding of how dietary interventions can be optimized through microbiome-targeted strategies for promoting human health and preventing chronic diseases.

Dr. Yiming Feng
Dr. Xiaohong Sun
Guest Editors

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