Insight into the relationship between metabolite dynamic changes and microorganisms of sea urchin (S. intermedius) gonads during storage

•HTS and metabolomic based on LC-MS/GC–MS of sea urchin gonads were performed.•Dominant genus transformed from Ralstonia to Aliivibrio during storage.•GC–MS based metabolites enriched in valine, leucine and isoleucine biosynthesis.•LC-MS based metabolites enriched in alanine, aspartate and glutamate metabolism.•Aliivibrio had a great influence on the production of differential metabolites. Sea urchin gonads have high nutritional value and degenerate rapidly during storage. Previous assessment of the freshness of sea urchin gonads was based on experience without valid biochemical indicators. Thus, the current study is to find biochemical indicators representing the freshness of sea urchin gonads. Results showed that the dominant genera of sea urchin gonads were changed from Psychromonas, Ralstonia, and Roseimarinus to Aliivibrio, Psychrilyobacter, and Photobacterium. The differential metabolites of sea urchin gonads were mainly produced through amino acids metabolism. Among them, GC-TOF-MS based differential metabolites had the greatest enrichment in the valine, leucine and isoleucine biosynthesis pathway, while LC-MS based differential metabolites had the greatest enrichment in the alanine, aspartate and glutamate metabolism pathway. The growth of dominant genus (Aliivibrio) had a great influence on the production of differential metabolites. These results will provide valuable information for accurately judging the freshness and shelf life of sea urchin gonads.