Extended Data Fig. 1: Antimicrobial BGCs and defense genes are enriched in accessory genomes.
From: Intraspecies warfare restricts strain coexistence in human skin microbiomes
(a) We constructed a pangenome for S. epidermidis isolates in our collection and annotated genes and biosynthetic gene clusters (BGCs). Antagonism-related BGCs were more frequent in accessory genomes, whereas metabolism-related BGCs were found in the core genome. (b) We identified regions of the genome with copy number variation within a lineage, indicating recently gained or lost regions. We compared the relative enrichment of Clusters of Orthologous Gene (COG) terms and hits from functional annotation databases among genes in the core genome and recent gain/loss regions. (c) As in B, but comparing genes in the core and accessory genomes. COG categories denoted in blue are metabolism associated, whereas antimicrobial production and resistance genes may be found in red categories. Significant enrichment in a two-sided Fisher’s Exact test is indicated by an asterisk (one for naive P-value < 0.05, two for Bonferroni corrected P-value < 0.05), and the number of genes annotated in each category is indicated to the right of the figure.
