Infectious bursal disease virus (IBDV) replicates in the gut associated lymphoid tissue and alters the gut microbiome of chickens

Infectious bursal disease virus (IBDV) is a member of the Birnaviridae family that infects B cells in chickens, leading to immunosuppression and mortality. Immunosuppression is known to exacerbate the colonisation and shedding of zoonotic gut bacteria, for example Campylobacter jejuni, Salmonella Enteritidis and Escherichia coli, for reasons that are poorly understood. In order to address this, we infected groups of chickens (n=6) with either a classical strain (F52-70) or a very virulent strain (UK661) of IBDV. At 3 days post-infection, both strains were found to replicate in the gut-associated lymphoid tissue of thecaecaltonsils. 16 s rRNA sequencing revealed that in birds infected with IBDV, regardless of strain, there was a decrease in bacterial diversity in the caecal tonsils, but an increase in diversity of bacteria shed from the cloaca. Secretary IgA binding to commensal bacteria is known to influence the composition of the microbiome, and we speculate that IBDV alters the repertoire of sIgA thereby altering the microbiome composition. Interestingly, we found the number of clostridial species was reduced following IBDV infection. Clostridial species have been shown to induce Treg populations in mice and we speculate that IBDV-mediated changes in the microbiome affect the population of different immune cells in the mucosa. Taken together, we hypothesise that IBDV infection directly affects the B cell population and indirectly affects other immune cell populations in the gut and alters the gut microbiome, which leads to a more favourable environment for zoonotic bacterial infections to colonise.