Free-range versus conventional: A comparison of microbial composition and Campylobacter contamination in broiler...

Farming systems are known to significantly influence gut microbiota composition and Campylobacter colonization in live broilers. However, little is known about how these effects persist or change after slaughter, particularly in shaping the carcass microbiota. This study investigated the occurrence and enumeration of Campylobacter, the overall bacterial community structure in carcasses from conventional and free-range broilers, and the influence of slaughter batch timing (early versus late) on contamination and microbiota composition. A total of 314 post-chilling carcass samples were analyzed: 160 from conventional and 154 from free-range production systems, each obtained from two slaughterhouses specialized in their respective production methods. On each sampling day, half of the carcasses were collected from the first slaughtered batches, and the other half from the last. Campylobacter occurrence was higher in free-range carcasses (96.2 %) than in conventional ones (75 %), although mean counts were greater in conventional carcasses (1.8 log₁₀ CFU/ml) compared with free-range carcasses (1.3 log₁₀ CFU/ml). The timing of slaughter batches did not significantly affect Campylobacter contamination levels. Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) revealed a clear separation between the carcass microbiota of conventional and free-range broilers. Conventional carcasses were enriched in common gut- and processing-related genera, including Aliarcobacter, Lactococcus, and Pseudarthrobacter. Free-range carcasses displayed higher abundances of gut-associated taxa, including Lysinibacillus, Comamonas, and Rikenellaceae RC9 gut group, as well as genera not typically associated with the broiler gut or processing environments (Ureibacillus, Pedobacter, Pseudoxanthomonas). Within conventional systems, early batches were dominated by bacteria typical of processing environments (Aliarcobacter, Chryseobacterium, Flavobacterium). In contrast, later batches showed increased abundances of gut-associated and spoilage genera (Clostridium, Bacillus, Romboutsia, Moraxella). In free-range carcasses, later batches showed a higher abundance of the thermotolerant and biofilm-forming Anoxybacillus. Overall, these findings highlight distinct microbial signatures and Campylobacter contamination patterns between production systems and emphasize that slaughter-related factors, particularly processing time, further shape carcass microbiota composition.