Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms

Abstract

Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR). The remaining rinsates underwent microbiome analysis using 16S rRNA gene fragments on an Illumina MiSeq and were analyzed by Quantitative Insights into Microbial Ecology (QIIME). The key stages of processing were determined to be at rehang, pre-chill, and post-chill as per the Salmonella Reduction Regulation (75 Fed. Reg. 27288-27294). The APC microbial data from rehang, pre-chill, and post-chill were mean log 4.63 CFU/mL, 3.21 CFU/mL, and 0.89 CFU/mL and EB counts were mean log 2.99 CFU/mL, 1.95 CFU/mL, and 0.35 CFU/mL. NGS of WBCR identified 222 Operational Taxonomic Units' (OTU's) of which only 23 OTU's or 10% of the population was recovered post-chill. Microbiome data suggested a high relative abundance of Pseudomonas at post-chill. Additionally, Pseudomonas, Enterobacteriaceae, and Weeksellaceae Chryseobacterium have been identified as potential indicator organisms having been isolated from all processing abattoirs and sampling locations. This study provides insight into the microbiota of commercial broilers during poultry processing.

Keywords: Pseudomonas; Salmonella; microbiome; next generation sequencing; poultry; slaughter.

FIGURE 1

Diagram of the broiler slaughter process. The stars represent sampling locations.

FIGURE 2

Bio-map of evisceration. The bacterial mean log CFU/mL counts for both Enterobacteriaceae and aerobic plate counts (APC).

FIGURE 3

All phylum present through rehang, pre-chill, and post-Chill.

FIGURE 4

Bio-map of microorganisms through evisceration when the genera were identified at all sampling locations and abattoirs.

FIGURE 5

Chao 1 rarefaction curve. The measure of richness within a community at each processing abattoir and testing location within the plant.

FIGURE 6

Operational Taxonomic Unit (OTU) rarefaction curves. The number of observed OTU’s versus the length of sequence read at each processing plant and testing location within the plant.

FIGURE 7

Beta diversity between sampling locations and individual processing abattoir. Weighted and unweighted UniFrac PCoA plots (A) Plant 1 weighted. (B) Plant 1 unweighted. (C) Plant 2 weighted. (D) Plant 2 unweighted. (E) Plant 3 weighted. (F) Plant 3 unweighted. Orange is for rehang, blue is for pre-chill, and red is for post-chill.

FIGURE 8

Beta diversity among Pseudomonas spp. between sampling locations and individual processing abattoir. Weighted and unweighted UniFrac PCoA plots (A) Plant 1 weighted. (B) Plant 1 unweighted. (C) Plant 2 weighted. (D) Plant 2 unweighted. (E) Plant 3 weighted. (F) Plant 3 unweighted. Orange is for rehang, blue is for pre-chill, and red is for post-chill.