Similar Carcass Surface Microbiota Observed Following Primary Processing of Different Pig Batches

Abstract

Bacterial contamination during meat processing is a concern for both food safety and for the shelf life of pork meat products. The gut microbiota of meat-producing animals is one of the most important sources of surface contamination of processed carcasses. This microbiota is recognized to vary between pigs from different farms and could thus be reflected on the bacterial contamination of carcasses at time of processing. In this study, the microbiota of 26 carcasses of pigs originating from different farms (i.e., batches) were compared to determine if an association could be observed between carcass surface microbiota (top and bottom) and the origin of slaughtered animals. The microbiota of the top and bottom carcass surface areas was analyzed by culturing classical indicator microorganisms (mesophilic aerobic bacteria, Enterobacteria, Escherichia coli, Pseudomonas, and lactic bacteria), by the detection of Salmonella, and by 16S rRNA gene sequencing. Culture results showed higher Enterobacteria, E. coli, and lactic bacteria counts for the bottom areas of the carcasses (neck/chest/shoulder) when compared to the top areas. Salmonella was not detected in any samples. Globally, 16S rRNA gene sequencing showed a similar composition and diversity between the top and bottom carcass areas. Despite the presence of some genera associated with fecal contamination such as Terrisporobacter, Escherichia-Shigella, Turicibacter, Clostridium sensustricto1, and Streptococcus on the carcass surface, sequencing analysis suggested that there was no difference between the different batches of samples from the top and bottom areas of the carcasses. The primary processing therefore appears to cause a uniformization of the carcass global surface microbiota, with some specific bacteria being different depending on the carcass area sampled.

Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse

“…As the slaughter process is thought to present very little variation, it is possible to hypothesize that the differences in the mean relative abundance as well as in alpha and beta diversity are mainly supported by the arrival of different inputs (carcasses) in the cutting room, by the staff working during these different days, and by differences in the application of washing and disinfection measures. However, a study by Braley et al, conducted in the same facility as our study, revealed no significant difference of microbiota between pig carcass batches [ 46 ]. The fact that the study conducted by Braley et al was realized during a short period of time (one day) and the sampling in our study took place at monthly intervals could explain these variations in the impact of time.…”

Slight Temperature Deviation during a 56-Day Storage Period Does Not Affect the Microbiota of Fresh Vacuum-Packed Pork Loins

“…The detection of Salmonella spp. was based on the methods used in previous studies [ 38 , 39 ]. Briefly, thawed samples were cultured on Modified Semi-Solid Rappaport-Vassiliadis Agar (MSRV) (Biokar diagnostic) as a selective enrichment step and two selective media: Brilliant Green Sulfa (BD Difco, Franklin Lakes, NJ, USA) agar and Xylose-Lysine-Desoxycholate (Biokar diagnostic) agar.…”

“…A 291 pb fragment of the V4 region of the 16S rRNA gene was amplified by PCR using universal primers 515F_III (5′-ACACTGACGAACTGGTTCTACAAGTGCAGCMGCCGCGGTAA-3′) and 806R_III (5′-TACGGTAGCAGAGACTTGGTCTGGACTACHUGGGTWTCTAAT-3′) (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). A 30 μL PCR reaction assessment was performed using the Platinum SuperFi PCR Master Mix (Invitrogen, Burlington, ON, Canada), as previously described [ 39 ]. The PCR program consisted of an initial denaturation at 95 °C for 5 min, followed by 25 cycles of amplification that included a denaturation step at 95 °C for 30 s, an annealing step at 55 °C for 30 s, an elongation step at 72 °C for 60 s, and a final elongation step of 10 min at 72 °C in a Mastercycler ® Nexus PCR (Eppendorf AG, Hamburg, Germany).…”

“…The cleaning and the analyzing of the sequences were completed using Mothur [ 40 ] version 1.43 following the MiSeq standard operational procedure ( , accessed on 31 July 2021), as previously described [ 39 ]. Forward and reverse reads were merged into contigs for each sample.…”

“…Alpha and beta diversity analyses were performed using RStudio (version 1.4.1103), according to the standard operating procedure (SOP) used in a previous study [ 39 ]. Data were first rarefied to the lowest number of sequences found in a sample to minimize the impact of uneven sequencing depth.…”