Comparison of 16S rDNA Next Sequencing of Microbiome Communities From Post-scalder and Post-picker Stages in Three Different Commercial Poultry Plants Processing Three Classes of Broilers

Abstract

Poultry processing systems are a complex network of equipment and automation systems that require a proactive approach to monitoring in order to protect the food supply. Process oversight requires the use of multi-hurdle intervention systems to ensure that any undesirable microorganisms are reduced or eliminated by the time the carcasses are processed into final products. In the present study, whole bird carcass rinses (WBCR) collected at the post-scalder and post-picker locations from three different poultry processing facilities (Plant A: mid-weight broiler processing, B: large-weight broiler processing, C: young broiler (Cornish) processing) were subjected to next generation sequencing (NGS) and microbial quantification using direct plating methods to assess the microbial populations present during these stages of the poultry process. The quantification of aerobic plate counts (APC) and Enterobacteriaceae (EB) demonstrated that reductions for these microbial classes were not consistent between the two sampling locations for all facilities, but did not provide a clear picture of what microorganism(s) may be affecting those shifts. With the utilization of NGS, a more complete characterization of the microbial communities present including microorganisms that would not have been identified with the employed direct plating methodologies were identified. Although the foodborne pathogens typically associated with raw poultry, Salmonella and Campylobacter, were not identified, sequence analysis performed by Quantitative Insights of Microbiology Ecology (QIIME) indicated shifts of Erwinia, Serratia, and Arcobacter, which are microorganisms closely related to Salmonella and Campylobacter. Additionally, the presence of Chryseobacterium and Pseudomonas at both sampling locations and at all three facilities provides evidence that these microorganisms could potentially be utilized to assess the performance of multi-hurdle intervention systems.

Keywords: indicator organism; microbiome; next generation sequencing; poultry; poultry processing.

FIGURE 1

Average Log APC (A,C,E) and EB (B,D,F) counts of rinsates collected at post-scalder and post-picker location for Plants A, B, and C. ^abLog values denoted with different letters were significantly different between the post-scalder and post-picker collection sites at P ≤ 0.05.

FIGURE 2

Chao 1 alpha diversity metrics for sampling locations within each facility. (A) represents richness measurements for Plant A OTUs. (B) represents richness measurements for Plant B OTUs. (C) represents richness measurements for Plant C OTUs.

FIGURE 3

OTU rarefaction curves depicting number of OTUs versus sequence depth for sampling locations within each facility. (A) represents Plant A observed OTUs. (B) represents Plant B observed OTUs. (C) represents Plant C observed OTUs.

FIGURE 4

Weighted and Unweighted UniFrac plots depicting OTU diversity between microbiome populations of rinsates collected at post-scalder and post-picker locations. Weighted plots consider the relative abundance values of the OTUs present, and unweighted plots are based on the number of unique OTUs. Weighted UniFrac plots for Plant A, B, and C are represented in left column (A,C,E), respectively. Unweighted UniFrac plots for Plants A, B, and C are represented in right column (B,D,F), respectively.

FIGURE 5

Relative abundancies of phyla represented by OTUs present at post-scalder and post-picker sites for Plant A, B, and C. OTUs at Plants A and B were representative of Proteobacteria, Bacteroidetes, and Firmicutes. OTUs at Plant C were representative of Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria.

FIGURE 6

Relative abundancies of OTUs at Plant A. (A) Post-scalder collection site. (B) Post-picker collection site. OTUs in bold were present at both sampling locations.

FIGURE 7

Relative abundancies of OTUs at Plant B. (A) Post-scalder collection site. (B) Post-picker collection site. OTUs in bold were present at both sampling locations.

FIGURE 8

Relative abundancies of OTUs at Plant C. (A) Post-scalder collection site. (B) Post-picker collection site. OTUs in bold were present at both sampling locations.