The world's increasing need for protein faces challenges in aquaculture production. New applications and tools will need to be added at every stage of the manufacturing line to attain this expansion sustainably, safely, and effectively. Utilizing experimental methods to increase aquatic animal production has become more common as aquatic biotechnology has advanced. High-throughput omics technologies have been introduced to address these issues, including transcriptomic, metabolomic, proteomic, and genomes. But it also faces many difficulties, like other food manufacturing industries. One of the best and most durable approaches to address these issues is probably to understand nutritional requirements and modify diet based on need. Molecular approaches are a subset of multiomics technology. Previously, most of the published work was devoted to the biochemical aspects of protein-lipid interactions in biological systems. In this review, we explore this idea and highlight various works that fall under the umbrella of nutrigenomics, with a particular emphasis on protein utilization and its interactions with carbohydrates and lipids.