Pairwise comparative analysis of differentially expressed genes (DEG’s) between R20291 and FM2.5, FM2.5varA and FM2.5varB.

For differential comparisons, we used an A (R20291) versus B (FM2.5, FM2.5varA, FM2.5varB) model with no additional covariates. Differential expression values were generated using DESeq2 [64] (v1.24) and the processed data visualised using Searchlight [65]. DEG’s were determined as those genes with an absolute log2-fold cut-off of 1 (positive values for relative upregulated genes and negative values for relative downregulated genes) and -adjusted p value of 0.05. Functional and metabolic pathways were implied by interrogation of the WP numbers assigned using the C. difficile annotated genome (NC_013316.1). Data is also shown for comparisons between FM2.5 vs FM2.5varA, FM2.5 vs FM2.5varB and FM2.5varA vs FM2.5varB. (XLSX)