Fig. 1

Dysbiosis of the nasal microbiome exacerbates influenza-induced respiratory disease. A Boxplot showing the Richness and Chao diversity index of nasal microbiota in dogs before (BAbx) and after (CAbx) antibiotic treatment. The data were analyzed by a two-way ANOVA test, Tukey’s HSD. B Principal coordinate analysis (PCoA) of microbiota communities utilizing Bray–Curtis distances for samples before and after antibiotic treatment. The boxplots below and left boxplots show the overall distribution of PCoA1 and PCoA 2 scores in each group. C A heatmap illustrating the differential relative contribution of KEGG pathways, predicted based on the microbiota composition at the sampling stages before (BAbx) and after (CAbx) antibiotic treatment. D Flowchart overview of the study design. E Changes in rectal temperature after intranasal challenge with influenza virus. F Changes in body weight after intranasal challenge with influenza virus. Rectal temperature and body weight data were presented as mean ± SEM, and a two-way ANOVA test was used for analysis. * p < 0.05, ** p < 0.01, and *** p < 0.001 indicate a significant difference between the WT and Abx groups. # p < 0.05, ## p < 0.01, and ### p < 0.001 indicate a significant difference between the Nor and WT groups. G Disease severity scores in dogs infected with influenza virus 8 dpi in the Nor, WT, and Abx groups. H Virus titers in the nasal swabs at 1, 3, 6, and 8 dpi and lungs at 8 dpi. I Representative images of gross anatomy of the lung and histopathological appearance of H&E-stained nasal, tracheal, and lung tissues in dogs infected with influenza virus at 8 dpi. Both the WT and Abx groups exhibited interstitial pneumonia, characterized by the thickening of alveolar septa and infiltration of numerous inflammatory cells. J Histological scores of nasal cavities, tracheal, and lung tissues infected with influenza virus at 8 dpi in the Nor, WT, and Abx groups. K Representative images of immunofluorescence staining of nasal cavity, trachea, and lung tissues infected with influenza virus at 8 dpi show viral nucleoprotein (NP) in red and cell nuclei stained blue with DAPI. L Mean fluorescence intensity (MFI) of NP in nasal cavity, trachea, and lung tissues infected with influenza virus at 8 dpi