Chicken cecal microbial functional capacity and resistome differ by age and barn disinfection practice

Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Previous studies showed that chemical disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functionality. The current study compared the effects of chemical disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after 2 production cycles at 7 barns. Shotgun metagenomic sequencing performed on cecal contents collected at day 7 and 30 also allowed evaluation of age-associated characteristics of microbiome. Age of the chickens had the largest effects on the resistome, with younger birds having increased relative abundance of total ARGs (P<0.05) and differences in resistance mechanism, however, functional and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically-disinfected barns had decreased functional capacity related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically-disinfected condition (FDR-P<0.05), suggesting selection for stress resistance. Consistently, lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecal Helicobacter pullorum was observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P<0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial functionality and resistome. Importance This is the first study to evaluate the effect of sanitation practices on microbial functional capacity and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.