Extended Data Fig. 8: Alterations in the transcriptomic profiles of S. Tm and commensals vary between drug treatments.
From: Non-antibiotics disrupt colonization resistance against enteropathogens
a) KEGG pathways more represented than expected among genes that are up- and -downregulated in S. Tm after growth in drug-treated Com20 or pure culture compared to untreated Com20. Circle size represents the fraction of differentially expressed genes from DESeq2 analysis that map to a pathway, relative to the total number of differentially expressed genes. Values were calculated separately for upregulated and downregulated genes. Circle colors represent the adjusted P values from overrepresentation analysis. Pathways grouped by their KEGG category. b) Number of genes in the 20 % of highest expression on each member of Com20 upon treatment or in untreated Com20; red bar indicates the number of genes in the set of stress-related markers identified by Avican et al.22. c) Fraction of the top 20 % most expressed genes that are stress-related marker genes22 in each of the 20 species of Com20 across controls and treatments; in other words, from b): red bar/(red bar + gray bar). Red horizontal and vertical lines represent mean ± 1 s.e.m. P values with Benjamini-Hochberg correction from one-tailed t-tests.
