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Spleen, liver and mesenteric lymph nodes were harvested on day 5 of C. difficile infection. Bacterial 16S rDNA was extracted using the PureLinkTM Microbiome DNA Purification kit (ThermoFisher Scientific) and gene levels were quantified by qPCR using primers complementary to Eubacteria 16S rDNA conserved region (Supplementary Table S2). Bacterial load was determined using an E. coli genomic DNA standard curve and the CFU/g tissue was normalized (gene levels/sample weight).
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