16S rDNA Microbiome of Whole Bird Carcass Rinses Collected with nBPW and BPW from a Commercial Broiler Processing Facility

In 2016, the United States Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) established guidelines which modified the Buffered Peptone Water (BPW) rinsate material to include additional compounds that would better neutralize residual processing aids and allow for better recovery of sublethal injured Salmonella spp. cells. While the compounds added improved the recovery of Salmonella spp., specific data to understand how the new rinsate, neutralizing Buffered Peptone Water (nBPW), effected the recovery of other microorganisms (including Campylobacter spp. and indicator microorganisms) was not initially available. This study was conducted to determine how the rinse solutions (BPW or nBPW) used in whole bird carcass sample collections could influence microbiome compositional profile of collected rinsates and in turn, how those compositions could impact results obtained from culturing methodologies. Carcasses exiting a peroxyacetic acid (PAA) finishing chiller were rinsed in 400 mL of either nBPW or BPW and resulting rinsates were analyzed for prevalence of Salmonella spp. and Campylobacter spp. as well as quantitative levels of aerobic bacteria (APC) and Enterobacteriaceae (EB). Genomic DNA was extracted from the rinsates, petrifilm, agar plates and enrichment media and the V4 region of the 16S rDNA was amplified using duel-indexed primers. Resulting amplicons were normalized, pooled and sequenced on an Illumina MiSeq. Demultiplexed sequences were uploaded and analyzed in QIIME2.2019.7 and diversity metrics, alpha and beta, along with operational taxonomic unit (OTU) compositions were evaluated. Cultured microbiological methods indicated significant differences (P < 0.05) in APC levels of the two rinsates, but no significant differences in EB, Salmonella spp. or Campylobacter spp. prevalence. However, there was a marked difference between the microbial diversity of the two rinsate types and the subsequent selective and non-selective medias used for the cultivation of APC, EB and Campylobacter spp. (P < 0.05). Additionally, several OTUs, including Streptococcus, Lactobacillus, Aeromonas, Acinetobacter, Clostridium, and OTUs belonging to Enterococcaceae, Burkholderiaceae, and Staphylococcaceae were identified as differentially abundant in paired populations. These results highlight that the media type used in a WBC rinse causes proportional shifts in the microbiota, which can lead to differences in results obtained from cultured microbial populations.