Preliminary association between infectious bronchitis virus viral load and the tracheal microbiome of broiler chickens

Infectious bronchitis virus (IBV) is a major respiratory pathogen in poultry, yet its impact on the tracheal microbiota under field conditions remains insufficiently understood. This study investigated the effects of IBV infection intensity on tracheal microbial diversity and composition in broiler chickens using 16 S rRNA gene sequencing. A total of 200 tracheal samples were collected from commercial farms and screened using RT-qPCR. Samples were stratified into high, low, and negative viral load groups based on cycle threshold (Ct) values, and a representative subset was selected for microbiome analysis. Alpha diversity analysis revealed a significant reduction in microbial richness (Observed species and Chao1 indices; q < 0.05) in the low-viral-load group compared with controls, while Shannon diversity remained unchanged, suggesting a selective loss of rare taxa. In contrast, no significant changes in alpha diversity were observed in the high viral load group. Beta-diversity analysis based on Bray-Curtis dissimilarity (PERMANOVA) revealed significant differences in microbial community composition among different viral load groups. Taxonomic analysis showed stability at the phylum level, with more pronounced shifts at the genus level. These findings indicate that IBV infection induces selective and load-dependent alterations in the tracheal microbiota. Notably, treating infection as a binary variable may obscure ecologically meaningful and biologically relevant microbial shifts. This preliminary field study provides evidence that IBV viral load is associated with differences in the respiratory microbiome of broiler chickens under field conditions.