Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.

Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.