Fig. 2

Streptomycin treatment of mice induces a shift in community structure of the large bowel microbiome. Mice were mock-treated (n = 8) or received a single dose of streptomycin (n = 8) and bacterial communities in the colon contents were analyzed 3 days later. a Principal coordinate analysis of 16S rRNA gene amplicon sequencing of colon contents from mice. b Box plot of weighted unifrac distance between mock and streptomycin treated mice (P value = 0.002). c LEFSE cladogram displaying taxa enriched in mock-treated mice (red) or in streptomycin-treated mice (green). Taxa enriched within higher level taxa are indicated by a darker shading. d Box plots showing the relative abundance of Clostridia and Erysipelotrichia in mock-treated and streptomycin-treated mice. e Significantly increased and decreased amplicon sequence variants by class in streptomycin-treated mice relative to mock-treated mice (FDR corrected P value ≤ 0.05). f Relative abundance (left pie chart) and taxonomic diversity of ASVs (right pie chart) in mock-treated mice at the class level