Metagenomic assessment of the microbial diversity of swine carcasses

Contamination, cross-contamination, or carcass recontamination can mainly occur along the slaughtering processes due to contact between animals during their transportation, steps of slaughter carcass preparation, slaughterhouse environment, clothing, and poor slaughter and hygiene practices [1]. Evaluating the microbiological profile is important to verify hygiene conditions during the slaughter processes and ensure the food safety of the final product [2]. The purpose of this study was to characterize the microbial community of swine carcasses and environmental samples - knives and drains - using a metagenomic approach. Gauze swabs were used to collect samples from drains and from five animals before and after evisceration, and water from the knives sterilizer was collected in sterile tubes before and after eviscerations. Samples were prepared for Illumina Sequencing by 16S rRNA gene amplification of the bacterial community. All 16S rRNA data were analysed with Kraken v1 using the pre-built MiniKraken 8Gb database (https://ccb.jhu.edu/software/kraken/) with default parameters. Twenty-five genera with abundance above 1% were found. The most abundant genus on carcasses was Anoxybacillus (52% of the total microbiome) and on environmental samples Oenococcus (15%). Enterobacteriaceae were detected in 13 collected points (prevalence ranging from 0.001% to 0.02%), with different genera found: Citrobacter (18.0%), Klebsiella (14.0%), Erwinia (12.1%), Enterobacter (9.99%), Trabulsiella (5.99%), Providencia (4.0%), Serratia (4.0%), Salmonella (4.0%) and Morganella (1.99%). It is important to highlight that Salmonella spp. was found in only two samples, one from the carcass and the other from the drain sampled on the same day. Other genera of interest in food microbiology were also detected, namely, Pseudomonas, Lactobacillus, Campylobacter, Clostridium, Bacillus, Staphylococcus, and Lactococcus. Such diversity suggests possible interventions to extend shelf life hampered by the microbial consortia with pork products. Otherwise, it may be useful for developing microbial traceability to a slaughterhouse.