ASVs differentially enriched on days 120 p.i.

and 160 p.i. in the feces of wild-type S. Typhimurium-infected control mice (no co-housing) compared to mice co-housed with a CONXmouse. ASVs were identified in samples from mice on day 120 and 160 p.i. (n = 6 mice for each, wild-type S. Typhimurium kept under hygienic isolation and mice co-housed with CONX animals; from Fig 3). Measures of within-sample diversity, beta-diversity and order or phylum diversity are shown in Figs 3E and S9. Significantly enriched ASVs, determined by a Wald test are ranked by log2 fold change (S.Tm and S.Tm + CONX). Shown are ASVs that are significantly more abundant in S.Tm with a padjusted cut-off of p < 0.05 and a log2 fold change cut-off of >1 (indicated as a blue shade in the table). BaseMean represents the average read counts that were normalized by size factors over all samples.
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