Impacts of novel duck reovirus infection on the composition of intestinal microbiota of Muscovy ducklings

Novel duck reovirus (NDRV) is pathogenic to young ducks, which is characterized by hemorrhagic spots and necrotic foci of the livers and necrotic foci of spleens. However, the effect of NDRV infection on the composition of the hosts intestinal microbiota remains poorly understood. In this study, three-day-old Muscovy ducklings were inoculated with either the virulent NDRV strain NP03 or sterile Hank's solution. Through Illumina MiSeq sequencing, the whole cecal microbiota of healthy and NDRV infected ducklings was examined. The results showed that the gut microbiota was mainly dominated by Firmicutes, Proteobacteria and Bacteroidestes in both healthy and NDRV infected ducks. NDRV infection altered the relative abundance of bacteria. Specifically, families Ruminococcaceae and Lachnospiraceae were remarkably reduced, whereas Escherichia_Shigella belonging to family Enterobacteriaceae was significantly increased. Collectively, NDRV infection in Muscovy ducks resulted in a shift of the gut microbiota, including a net loss of probiotic bacteria with a compensatory expansion of pathogenic bacteria. These results provide new insights into the potential pathogenic mechanisms of NDRV.