The freshwater fish, serving as a significant source of high-quality aquatic animal protein, play a pivotal role in ensuring the national food security in China. Refrigeration is commonly employed for the storage and preservation of freshwater fish, however, protein degradation and texture deterioration result in a decline in sensory quality and a reduction in shelf life. These factors significantly impede the development of the fresh and chilled freshwater fish industry (Bao et al., 2020). It is reported that growth and metabolism of SSOs are the primary factors causing fish spoilage (Gram et al., 2002). The myofibrillar protein in fish is susceptible to degradation under the action of both endogenous and microbial enzymes, leading to a decline in muscle quality such as affecting the texture and water-holding capability (WHC) (Delbarre-Ladrat et al., 2006; Tang et al., 2020; Zhuang et al., 2023a). Protein degradation is an important biochemical process during fish storage because it causes the softening of fish texture and produces soluble nitrogen-containing compounds that can facilitate microbial growth. During chilled storage, fish protein undergoes depolymerization and degradation, which affects the quality and functional properties of fish flesh. It has been reported that the microbial proteases secreted are the principal cause of protein degradation besides endogenous enzymes (Huang et al., 2021; Hultmann and Rustad, 2004). Therefore, elucidating the mechanisms of SSOs-induced fish protein degradation is crucial to uncover the inner relations between protein degradation and related quality changes.

In our previous study, Pseudomonas psychrophila and Shewanella putrefaciens were found dominant in spoiled freshwater fish flesh (Jia et al., 2018, Jia et al., 2019a), and they are also the main microbial species that cause spoilage of meat and dairy products (Gram and Melchiorsen, 1996; Paździor, 2016; Sterniša et al., 2019; Tomaś et al., 2021). The spoilage potential of these microorganisms is closely connected to various intricate metabolic alterations that result in fish flesh deterioration including texture deterioration and water loss (Gram and Henrik, 1996). The process of fish spoilage caused by microbial activity has been extensively studied. However, there have been limited reports on the integration of whole-genome mining and SSOs inoculation to investigate the protein degradation processes specifically associated with fish spoilage. Therefore, this research focuses on protein degradation which is the frontier problem during fish chilled storage to clarify the specific roles of P. psychrophila and S. putrefaciens in fish texture deterioration, elucidate the protein degradation characteristics of fish caused by microbial action, annotate the gene functions of two strains based on gene sequences, and screen out the genes related to fish protein degradation to deepen our understanding of the spoilage mechanism of spoilage bacteria. This study will provide valuable insights into the fundamental theory underlying fish protein degradation.