Fig. 1

Disease outcomes and beta diversity of lung and intestinal microbiota following infection with SARS-CoV-2 Wuhan or SARS-CoV-2 Omicron. (a) Schematic representation of the timeline of the murine experiments. Six-week-old K18-hACE2-tg mice were intranasally exposed to phosphate-buffered saline (PBS, non-infection), SARS-CoV-2 Wuhan, or SARS-CoV-2 Omicron (n = 4 mice each group). (b) Survival rates of the experimental mice. (c) RNA copies of viral N1 in 1 µg of lung tissues total RNA from experimental mice were measured using qPCR. (d, e) Lung and tracheal tissues from experimental mice were harvested at 5 dpi or 10 dpi for histological analysis. Representative images are shown of the lungs (d) and trachea (e). Scale bars in the lung images indicate 50 μm in the first line and 10 μm in the magnified images in the second line. Scale bars in the tracheal images indicate 5 μm. (f) Schematic of the timeline used for sample collection. Six-week-old K18-hACE2-tg mice were intranasally exposed to PBS (non-infection), SARS-CoV-2 Wuhan, or SARS-CoV-2 Omicron. Lung and fecal samples from the non-infection and Wuhan groups were collected at 5 dpi, and samples from the Omicron group were collected at 5 dpi and 10 dpi. (g, h) PCoA plots for lung (g) and fecal (h) samples from the experimental mice. Data in c were analyzed using one-way ANOVA and error bars indicate the mean ± SEM. Data in g and h were analyzed using PERANOVA. The comparison results of infection pathology (a–e) are representative of two independent experiments