LC-MS/MS-based peptidomics and metabolomics reveal different metabolic patterns of common spoilage bacteria in grass carp flesh

Grass carp are highly perishable under the action of spoilage bacteria including Aeromonas rivipollensis, Pseudomonas putida, and Shewanella putrefaciens. However, the metabolic characteristics of the three bacteria in degrading fish proteins and small molecular nutrients are unclear. In this study, we used LC-MS/MS-based peptidomics and metabolomics to detect peptides and small molecular metabolites in grass carp flesh inoculated with the three bacteria. The peptidomic results showed that A. rivipollensis and S. putrefaciens induced an overall increase in the molecular weight of peptides in grass carp flesh. S. putrefaciens tended to hydrolyze peptide bonds composed of at least one hydrophobic amino acid whereas A. rivipollensis and P. putida preferred hydrolyzing Xaa-serine bonds. The metabolomic results showed that amino acid metabolism and nucleotide metabolism are among the most enriched pathways of differential metabolites. P. putida and S. putrefaciens were active in decomposing amino acids and nucleosides, respectively. Besides, lipid metabolism also plays an important role in grass carp spoilage, representing as the degradation from phosphatidylcholine to lysophosphatidylcholine by the three bacteria. To conclude, this study revealed distinct metabolic characteristics of the three bacteria in degrading proteins and small molecular metabolites, and thus contribute to the understanding of fish spoilage mechanisms.