Fig. 1. SARS-CoV-2 infection causes gut microbiome alterations in mice.
K18-hACE2 mice were infected intranasally with 0 or 104 PFU of SARS-CoV-2. Fecal samples for microbiome analyses were collected daily from day 0 (before infection) until sacrifice; mice were sacrificed on days 5–7. Results show pooled data from three independent experiments with n = 3–5 mice per group. a Timelines of fecal microbiota composition measured by 16S rRNA gene sequencing. Bars represent the composition of the 15 most abundant bacterial families per sample for each day, blocks of samples correspond to an individual mouse’s time course from day 0 to day 6, as exemplified for the first mouse. b α-diversity (inverse Simpson index) per infection group in the beginning (tstart, n = 13 each for control and infected) and at the end (tend, n = 13 each for control and infected) of the experiment (n.s.: non-significant, **: p < 0.01, one-tailed, paired t-test; boxplots show median and quartile ranges). Comparison between infected and non-infected mouse microbiomes at the end of the experiment. c Principal coordinate plot of bacterial compositions in samples collected prior to infection (tstart, top) and at sacrifice (tend, bottom) of the experiment (Bray Curtis dissimilarity). d log10-relative family abundances at the final time point; boxplots show median and quartile ranges, whiskers extend to 1.5 times max- and min- quartile values, n.s.: not significant; *: p value < 0.05; **: p value < 0.01; ***: p value < 0.001; two-sided Wilcoxon rank-sum tests (n = 13 each for control and infected). e Analysis of microbiome composition trajectories in infected mice. Regression coefficients of the estimated changes in family abundances per day in mice infected with 104 PFU were obtained from linear mixed effects models with varying effects per mouse and per cage (only significant coefficient results shown, abbreviations and colors as per the bacterial family legend; Red: separate, analogous analysis for phylum Proteobacteria trajectories).