Carcass surface microbiota analysis for investigating bacterial communities evolution during pigs processing

By using culture-independent method, this study investigated how the pig carcass surface microbiota is evolving from days to days during processing in a slaughterhouse in Quebec. The carcass surface microbiota of 64 pig batches was characterize at different times point during four processing weeks before and after the cooling. The microbiota of the top and bottom carcass surface areas was analyzed by 16S rRNA amplicon sequencing, combined to classical enumerations of indicator (mesophilic aerobic bacteria, Enterobacteria, Escherichia coli, Pseudomonas and lactic bacteria) and the detection of Salmonella spp. Salmonella spp was detected in 11 pigs carcasses areas. Globally, the results of the comparison of carcasses areas show a higher level of bacterial counts on bottom areas, while sequencing results showed a higher bacterial diversity on top areas before cooling. After cooling, diversity of the microbiota decreased on the top and bottom areas but most of detected bacteria remains and cooling did not allow to reduce considerably bacterial counts on bottom areas. During normal commercial primary processing, pig carcass surface microbiota composition and diversity evolve in time and appears different between day shifts and visits during four weeks.