Longitudinal RNA Seq analyses reveal the prominent role of Vagococcus in broiler meat spoilage microbiome

Background Raw broiler meat products are highly perishable, and microbial activity is the main factor limiting their shelf lives. The spoilage microbiomes of broiler meat products have been studied mainly using traditional culturing methods and 16S rRNA gene amplicon sequencing, neither of which can show the activity of whole microbiome. Previous metatranscriptomic research of broiler spoilage has also remained limited to specific spoilage organisms rather than entire microbiomes. Results Our longitudinal study of broiler meat spoilage discovered the successions of active bacterial microbiomes and metabolic pathway activities of spoilers at 4C and 6C. Samples taken daily were subjected to metatranscriptomic analyses in combination with non-targeted metabolomic, traditional microbiology, and sensory analyses until advanced spoilage took place. Carnobacterium divergens, Carnobacterium maltaromaticum and Vagococcus proximus were the most active species at both temperatures. Carnobacteria are known poultry spoilers whereas Vagococcus proximus, a species recently described, played an unexpected active role in the microbiome. It became dominant in samples stored at 6C and its activity increased also at 4C after the use-by date. Central carbohydrate metabolism was the most common KEGG orthology pathway module of the microbiome at both temperatures. C. divergens and C. maltaromaticum showed stable metabolic profiles during the spoilage process, whereas V. proximus displayed a shift from high ATP synthesis activity to increased fatty acid and carbohydrate metabolism when spoilage advanced in samples stored at 4C. Non-targeted metabolomics showed similar metabolomic trends across both temperatures. At 6C, time-dependent changes were generally more pronounced, and the spoilage markers tyramine and spermidine showed greater accumulation. Conclusions As expected, the rate of spoilage is higher at 6 than 4C, however we did not anticipate a similar overall trajectory of the spoilage processes. Our results link V. proximus as a key active spoiler in broiler meat and demonstrate the efficacy of using RNA-seq together with metabolomics to decode the function of a meat spoilage microbiome. This demonstrates that spoilage microbiomes consist of active species we have been neglecting due to the technological limitations of the standard methods. Future studies targeting to the metabolism and detecting of Vagococcus are warranted.