FIG 6.

Pan-genome and prophage content. The total numbers of genes in the pan-genome (A) and core genome (B) are plotted as a function of the number of genomes sequentially added (n = 207). (A) The pan-genome size is calculated at 10,378 genes at n = 207 and displays characteristics of an open genome: (i) the trajectory of the pan-genome increases unboundedly as the number of genomes are added, and (ii) B_pan (≈γ [55]) was estimated as 0.46 (curve fit, r² = 0.999). Box plots indicate the 25th and 75th percentiles, with medians shown as horizontal lines and whiskers set at the 10th and 90th percentiles. (B) Consistent with an open pan-genome, the core genome curve (r² = 0.985) converges to 2,058 genes at n = 207, where an average of 16 new strain-specific genes are contributed to the gene pool. Overall, the core genome accounts for just 19.8% of the total gene repertoire. (C) Summary of intact prophage content found in 207 C. difficile strains of ST11 and ST258. More prophages were found in LCT⁻ RTs versus LCT⁺ RTs, the RT127 lineage versus the RT126 and -078 lineages, and veterinary versus clinical strains (P < 0.001).