Molecular Interfaces in Animal Nutrition: From Gut Microbiomes and Transcriptomics to Sustainable Feed Strategies

Dear Colleagues,

The growing demand for sustainable, efficient, and high-quality animal production has driven a paradigm shift from classical nutritional approaches toward molecular-level interventions. Understanding how diet interacts with the animal's genome, transcriptome, and gut microbiome—collectively termed nutrigenomics and meta-genomics—offers unprecedented opportunities to optimize cattle and waterfowl performance, enhance meat quality, and modulate protein and lipid metabolism.

However, significant challenges remain. Mycotoxin contamination continues to threaten feed safety and animal health, while the need for circular agriculture demands innovative valorization of agricultural waste. Solid-state fermentation has emerged as a powerful biotechnological tool to upgrade low-value agro-industrial residues into functional feeds, yet the underlying molecular responses in target species remain underexplored. Furthermore, plant extracts are gaining traction as natural feed additives, but their precise effects on host gene expression, intestinal microbial ecology, and metabolic pathways require systematic elucidation.

This Special Issue aims to gather cutting-edge research that integrates transcriptomics, metagenomics, and nutrigenomics to address key questions in ruminant and waterfowl nutrition. We invite contributions that explore the following:

• Multi-omics dissection of protein and lipid metabolism in cattle and waterfowl in response to alternative feed sources;
• Molecular mechanisms by which plant extracts and fermented agricultural waste improve feed efficiency, meat quality (e.g., marbling, fatty acid profile, tenderness), and gut health;
• Metagenomic and transcriptomic signatures of mycotoxin exposure and mitigation strategies (e.g., biodegradation via solid-state fermentation);
• Solid-state fermentation as a tool to enhance the nutritional and nutraceutical value of agricultural waste, with emphasis on changes in microbial communities and bioactive compound profiles;
• Comparative nutrigenomics between ruminants (e.g., rumen epithelium transcriptome) and waterfowl (e.g., liver and muscle lipid metabolism), revealing species-specific adaptations.

We welcome original research articles, reviews, and short communications that apply molecular tools (RNA-seq, metagenomic sequencing, qPCR, proteomics, metabolomics) to advance sustainable animal production. By bridging fundamental molecular science with applied nutrition and waste valorization, this Special Issue will provide a framework for developing next-generation, microbiome-smart, and circular feed strategies that simultaneously improve animal health, product quality, and environmental footprint.

Dr. Ali Mujtaba Shah
Dr. Rui Hu
Guest Editors

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