Abstract / Summary
In the poultry industry, infection with low-pathogenicity avian influenza viruses is often accompanied by atypical clinical manifestations, such as diarrhea, the underlying mechanisms of which are yet to be elucidated. In this study, ten chickens were randomly divided into two groups (n = 5 per group). One group is infected with the H9N2 subtype of avian influenza virus to simulate the clinical infection. Bronchioalveolar lavage fluid (BALF), as well as cecal and colonic contents samples, was collected at 5 days post inoculation (dpi), and 16S rRNA sequencing was employed to analyze the alterations of the pulmonary and intestinal microbiota. Our results showed that H9N2 infection did not significantly alter the alpha or beta diversity of either the gut or lung microbiota. LEfSe analysis revealed that the infected group exhibited enrichment of Oscillospira and Fournierella in the gut and Delftia and Pelomonas in the lung, whereas the control group showed enrichment of Bacteroides, Enorma, Anaerostignum, and Collinsella in the gut and Mycoplasma in the lung. Procrustes analysis showed no significant overall structural association between the two niches, while Spearman correlation analysis identified 54 significant cross-site microbial correlations. BugBase analysis indicated that the lung microbiota in the infected group exhibited significantly enhanced phenotypes related to potential pathogenicity, Gram-negative status, and stress tolerance. Collectively, these findings suggest that H9N2 may reshape the composition, function, and cross-site interaction networks of specific microbial taxa. Viral infection may be associated with cross-site alterations in the gut and lung microbiota via the “gut-lung axis”, with gut microbiota perturbations potentially influencing pulmonary susceptibility to secondary infections. This highlights the gut microbiota as a potential target for modulating respiratory pathogen colonization and reducing antibiotic use, while providing a novel theoretical basis for understanding the gut-lung axis in avian influenza infection in poultry.