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Disinfectant usage in barn cleaning alters the gut microbiome and increases carriage of Campylobacter jejuni in broiler chickens

2022 CPRF,Health & Immunity
Biosecurity is important to maintain flock health in broiler chicken production. Currently, Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection; FD) and may wash with water (water-wash; WW) between flocks throughout the year, though many choose to disinfect between each flock. We hypothesized that FD would impact microbial functional capacity and inadvertently increase the likelihood of pathogen transmission. To test this, we conducted a cross-over experiment over four production cycles in seven commercial chicken barns to compare WW and FD focusing on the broiler performance, microbial composition, function and cecal short-chain fatty acids (SCFAs). Unpaired student’s t test showed that the 30-day body weighs (p = 0.22) and mortality rates (p = 0.91) were comparable between WW and FD. The 16S rRNA sequencing results suggested that the WW brought a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis p < 0.05), with significant reductions in C. jejuni abundance. In addition, the WW group showed increased cecal acetate, butyrate and total SCFA concentrations (p < 0.05), which were negatively correlated with C. jejuni abundance (Spearman’s correlation coefficient test; p < 0.05). Shotgun metagenomics sequencing and functional analyses revealed that 564 genes and 47 pathways were differentially abundant between FD and WW chickens. Consistent with increased SCFA levels, several complex carbohydrate degradation-related and pyruvate fermentation pathways identified in Helicobacter, Lachnoclostridium and Megamonas were more abundant in the WW group (empirical Bayes quasi-likelihood F-test, FDR-p < 0.05). The FD group showed enriched pathways including a fatty acid synthesis pathway harbored by E. coli (FDR-p < 0.1) and a UDP-N-acetyl-D-glucosamine biosynthesis pathway encoded by C. jejuni (FDR-p < 0.1). The results indicated that WW led to a gut microbiota with enhanced capacity for the production of SCFA, and reduced the risk of zoonotic transmission of C. jejuni in broiler production relative to FD in the absence of a disease challenge.
Tags :
barn cleaning,broilers,gut microbiome
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PhD Student

University of Alberta

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