Figure 5.

Type I IFN signaling promotes overrepresentation of Erysipelatoclostridium and reduces Roseburia in the intestinal microbiome after LCMV Cl13 infection. See also Fig. S5 and Table S10. C57BL/6 mice were infected with LCMV Cl13 and injected with isotype (IgG1) or anti-IFNAR-1 Ab (αIFNAR) i.p. and sacrificed at day 9 p.i. 16S rRNA gene amplicon sequencing was performed on colonic and cecal contents. (A) Alpha diversity by the Shannon diversity index. (B) Beta diversity PCoA with Unweighted UniFrac, Jaccard and Bray–Curtis distances. (C) Frequency of sequences at the phylum level at indicated time points. (D and E) Frequency of phylum Firmicutes divided by Bacteroidetes (D) or phylum Verrucomicrobia divided by Firmicutes and Bacteroidetes (E) for each individual mouse. (F) Songbird multinomial regression analysis of genera in IgG1-treated versus αIFNAR-treated Cl13-infected mice. X axes correspond to individual taxa. Taxa highlighted in red were consistently perturbed, in the same direction and with rank cutoffs of −0.5 and 0.5, after shotgun metagenomics analysis of an independent cohort of mice. UP indicates taxa up-regulated in αIFNAR-treated versus IgG1-treated Cl13-infected mice. Data in A–F are representative of one independent repeat by 16S rRNA amplicon sequencing, with n = 9–10 mice/group. (A and C–E) Averages ± minimum/maximum (A) or ± SEM (C–E). (B) Significance was computed with PERMANOVA (999 permutations). ns, not significant; PC, principal component.