Extended Data Fig. 9: Phenotypic variation among S. epidermidis.

(a) Lineages were grouped into phylogroups according to phylogenetic structure as described previously, see Extended Data Fig. 4g. On many participants, multiple phylogroups coexist on the face at the same time. (b) The agrD sequence was annotated for each lineage on each participant and classified into quorum sensing types. Again, we found that on many participants, multiple agr types coexist on the face at the same time. Co-residence between different phylogroups and between incompatible quorum sensing types suggest that there is not competitive exclusion on the basis of phylogenic dissimilarity or quorum sensing. (c) We measured growth rate in liquid culture in TSB for all isolates in our collection (Methods). We calculated the median growth rate for each isolate in a lineage. Bars denote standard deviation (from technical duplicates of biological triplicates). (d) Lineages that grow faster than other lineages in vitro (green) reach higher abundance on individuals (blue), Spearman’s rank correlation. Note that growth in vivo may vary significantly due to differences between nutrient composition of skin and TSB. (e) Lineages that antagonize a higher fraction of other lineages (red) do not grow faster or slower than other lineages (green), Spearman’s rank correlation. (f) The growth rate for each isolate of idiosyncratic lineages 20, 37, and 58 (technical duplicates of biological quadruplicates) is shown. Growth rate varies between vraFG mutants (indicated with *) and wild-type isolates of each lineage, but without a directional trend. Reversion mutants of 37 have faster growth rates than 37.3, leaving the basis of the vraFG mutations unresolved.