Figure S5.

Type I IFN signaling promotes overrepresentation of Erysipelatoclostridium and reduces Roseburia species in the intestinal microbiome after LCMV Cl13 infection. C57BL/6 mice were infected with LCMV Cl13 and injected with isotype (IgG1) or anti-IFNAR-1 Ab (αIFNAR) i.p., and shotgun metagenomic sequencing was performed on colonic and cecal contents on day 9 p.i. (A) Alpha diversity by the Shannon diversity index. (B and C) Beta diversity PCoA with Jaccard (B) and Bray–Curtis (C) distances. (D) Frequency of sequences at the phylum level at indicated time points. (E and F) Frequency of phylum Firmicutes divided by Bacteroidetes (E) or phylum Verrucomicrobia divided by Firmicutes and Bacteroidetes (F) for each individual mouse. (G) Songbird multinomial regression analysis of species in IgG1-treated versus αIFNAR-treated Cl13-infected mice. X axes correspond to individual taxa. The genera of the taxa highlighted in red were consistently perturbed, in the same direction and with rank cutoffs of −0.5 and 0.5, after 16S shotgun metagenomics analysis of an independent cohort of mice. UP indicates taxa up-regulated in αIFNAR-treated versus IgG1-treated Cl13-infected mice. Data are representative of one independent repeat by shotgun metagenomics with n = 9–10 mice/group. Data are shown as averages ± minimum/maximum (A) or ± SEM (D–F). Significance in B and C was computed with PERMANOVA (999 permutations). ns, not significant; PC, principal component.