Meta-Taxonomic Analysis of Poultry and Slaughterhouse Microbiota: A Comprehensive Examination of Resident Microbial Communities

Poultry is among the world's most consumed foods. From farm to fork, contamination is a common occurrence along the poultry processing chain. The final microbial profile of poultry meat, including pathogenic and spoilage microorganisms, is influenced by each step in this process. The consumption of contaminated poultry poses a significant threat to public health, as it is associated to infections caused by foodborne pathogens such as Campylobacter, Salmonella, Listeria monocytogenes and Arcobacter. To reduce clinical cases, it is crucial to comprehend the contamination pathway throughout the food process and characterize the microbiota present in production environments. This understanding is essential for the implementation of appropriate sanitization procedures. This research aims to evaluate the extent to which the skin and ceca of broilers contribute to the indigenous microbiota within a slaughterhouse. Furthermore, it seeks to elucidate how the persistence and distribution of Arcobacter spp. in the environment are influenced by the patterns of cross-contamination associated with these specific sources. Therefore, 16S-rRNA gene-based total DNA sequencing was performed to reconstruct environmental contamination pathways within a slaughterhouse. Broiler neck skin (BNS) and caecum (BC) were sampled during processing, while environmental swabs (SE) were collected from surfaces after disinfection. Meta-taxonomic analysis showed a significant influence of environmental contamination on the microbiota of chicken skin. At the highest taxonomic resolution, the sampling sources showed a distinct composition and distribution of the microbiota at the genus-species level. Arcobacter butzleri emerged as one of the most abundant species and was detected throughout the slaughterhouse, showing a higher prevalence compared to other Campylobacterota. It was uniquely and significantly associated with BNS and SE, while Helicobacter pullorum and Campylobacter jejuni were indicators of BC. Our findings have emphasised the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. The analysis conducted underlines the significance of early monitoring of food pathogens in the production chain, supported by meta-taxonomic analysis. Using these detection approaches, the presence of these pathogens could soon be considered an indicator of food safety and quality in slaughtered poultry.