Bacterial community identification in poultry carcasses using high-throughput next generation sequencing

Abstract

Poultry products are susceptible to contamination by pathogenic and spoilage bacteria during the slaughtering process. Molecular techniques have been used to assist in the identification of microorganisms in various microbiomes. The aim of this study was to identify bacterial components of the microbiome in poultry carcasses during the slaughter process, using high-throughput next generation sequencing (HT-NGS). Samples were collected from three slaughterhouses (A, B, and C) located in southern Brazil and included those taken from three points (initial, middle, and end) in the chiller tanks and two carcass pools (at the entrance to the clean area and after the final carcass packaging) at each establishment. A total of 104 carcasses were collected from each slaughterhouse. For this study, HT-NGS allows for a precise, quantitative and culture-independent microbiome assessment in poultry products. Three phyla (Firmicutes, Bacteroidetes, and Proteobacteria) were found in all establishments, and one phylum (Verrucomicrobia) was found only in Establishment A. Common set of genera (Anaerotruncus, Bacteroides, Campylobacter, Erysipelatoclostridium, Faecalibacterium, Lachnoclostridium, and Subdoligranulum) was identified in processing establishments along with the groups unique to a particular site. Pathogenic and spoilage bacteria, as well as other microorganisms that were not expected in poultry products, were detected by HT-NGS technique. The Shannon diversity index was the highest in Establishment B (2.40), followed by establishments C (1.98) and A (1.43). As we progressed through sample analysis, from the entrance of the clean area to the final carcass packaging area, we found significant reductions (p < 0.05) in the quantities of sequences of all phyla in establishments A and B. Significant differences (p < 0.05) in the quantities of sequences of all phyla were found between different stages in the slaughtering process. More stringent control procedures in establishments A and B were associated with reduced contamination even though all establishments followed the official sanitary standards. Our findings provide new insight into the chicken meat microbiome, and can be used in future studies to help ensure food safety in slaughterhouses.