Extended Data Fig. 5: Warfare by S. epidermidis strains is mediated by diverse and unannotated effectors.

(a) In order to check for shared mechanisms, the binary antagonism matrix was clustered by constructing dendrograms for antagonism and sensitivity (Methods). White boxes indicate antagonism by the producer spot against the receiver lawn. Red arrows indicate the lineages in our collection chosen for our mechanism screen, which include 18 lineages with high antagonism frequencies plus 2 negative controls (which lacked antimicrobial production genes but contained suspected prophage, denoted by yellow arrows). We chose representative receiver bait lineages using the dendrogram of sensitivity to ensure that all interaction patterns were captured. Note that for this analysis, unlike other analyses in this study (Methods), antagonisms from idiosyncratic isolates that exhibit intra-lineage variation were not excluded. Lineages denoted by cyan arrows did not inhibit many S. epidermidis, with the exception of idiosyncratic lineages 20, 37, and 58, which cluster with some S. hominis and S. capitis isolates, denoted by a cyan line. It is possible that the antimicrobials behind these interactions are intended to target non-epidermidis species. (b) We screened cells and filtered supernatants against a representative array of bait lawns chosen based on interaction profiles from above. Filtrates treated with heat or proteinase to degrade proteins and peptides, desalting to remove small molecules, or 1:10 dilution were also tested. Filtrates exhibited varied patterns, including antagonisms likely mediated by small peptide effectors (isolate 30.1) and some cell-associated antagonisms induced by neighbours (isolate 34.2) or both. (c) Some cell-associated antagonisms are iron-mediated, as indicated by the elimination of the interaction in media supplemented with excess FeCl₃ (see isolate 51.1). All tested isolates displaying iron-suppressible antagonisms cells contained a biosynthetic gene cluster (BGC) for a product similar to pulcherriminic acid, an iron-sequestering pigment molecule which sabotages the iron supply. (d) We annotated putative bacteriocin BGCs and found BGCs for known compounds (including gallidermin-like, epicidin-like, and lactococcin-like BGCs) as well as unknown compounds. However, we did not find a clear correspondence between BGC presence and the phenotype classified in our mechanism screen, potentially due to multiple inducible effectors being encoded in the genome, incomplete expression of BGCs in different media or environments, or targets not represented in our screen (for example Cutibacterium acnes). One isolate, 32.1, had an active prophage that occasionally produced distinct plaques in this assay, and was later isolated using mitomycin-C induction.