Infection with GI-19 lineage infectious bronchitis virus induces transient restructuring of the cecal microbiota with persistent predicted functional alteration in chickens

Infectious bronchitis virus (IBV), an avian gammacoronavirus, primarily targets the respiratory tract but also replicates in gut-associated lymphoid tissues, including the cecal tonsils, where its temporal impact on the adjacent cecal microbiota remains unclear. Specific-pathogen-free chickens were challenged with a field-derived GI-19 K-IId strain, and the cecal microbiota was profiled at 3, 5, 7, 10, and 15 days post-infection (dpi) via 16 S rRNA amplicon sequencing. Viral RNA persisted in the cecal tonsils throughout the 15-day period. Alpha diversity was significantly lower in infected birds across the experimental period, with values lowest at 5 dpi and higher thereafter, although this temporal pattern was not statistically supported. Infected birds also exhibited an altered overall community structure with increased inter-individual variability. This structural disruption peaked at 5 dpi, characterized by a transient expansion of Lactobacillaceae and a concurrent depletion of Ruminococcaceae , with no taxonomic differences detected at later time points. PICRUSt2 inference of functional potential from 16 S rRNA gene data predicted enrichment of bile acid biosynthesis pathways and of a KEGG pathway annotated from Staphylococcus aureus surface and secreted proteins at 5 dpi; the latter remained enriched through 10 dpi, over the same interval in which community structure remained altered. Because these predictions are derive from taxonomic composition, they reflect underlying compositional shifts rather than provide independent evidence of altered microbial function. These findings provide a high-resolution temporal framework of IBV-associated changes in the cecal microbiota during the acute phase of infection at a site where the virus replicates persistently.