Mesquite seed flour as a nutrient-rich alternative to fishmeal for common carp fingerlings (Cyprinus carpio): Environmental, growth performance, transcriptomic and intestinal microbiota responses

This study evaluated the potential of mesquite seed flour ( Prosopis laevigata ) as an alternative to fishmeal (FM) in the diets of common carp fingerlings ( Cyprinus carpio ). A mesquite diet (MD) was formulated containing 48.8 % mesquite flour, 24.4 % fishmeal and 20.7 % corn flour. Over a 45-day trial, 1000 fingerlings were distributed across four tanks (two tank replicates per diet). The carried-out methodology included growth parameters and water quality evaluation, RNA sequencing from liver tissue, and 16S sequencing of intestinal microbiota composition. Both MD and FM diets provided optimal water quality conditions for the growth and well-being of fish during the experiment. Growth performance resulted similarly between MD and FM, with no significant differences in weight gain (379.40 ± 232.55 % for FM and 335.08 ± 219.69 % for MD). Transcriptomic analysis revealed differentially expressed genes involved in lipid metabolism, particularly fatty acid degradation and PPAR signaling pathways. Intestinal microbiota evaluation indicated diet-specific modulation in microbial composition since differences in the relative abundance of shared species between diets was identified. Additionally, MD-fed carp showed unique bacterial species, such as Shewanella putrefaciens and Myxococcus xanthus , while FM-fed fish showed Shewanella hanedai and Archangium disciforme . This study represents the first multi-omics approach, incorporating transcriptomics and metagenomics, to evaluate the effects of mesquite meal supplementation in an aquaculture species as an alternative to fishmeal for enhancing aquafeed sustainability. • Mesquite and fishmeal diets showed no differences in carp growth performance. • Mesquite diet maintained optimal water quality for carp growth. • Bioactive compounds in mesquite diet modulated liver lipid metabolism. • Fatty acid degradation and PPAR pathways were enriched from mesquite supplementation. • Dietary mesquite polyphenols improved gut microbiota composition.