From 8 of these families, we obtained 4,055 genomes (top) from cultured isolates and clustered them into 89 distinct C. acnes lineages and 78 distinct S. epidermidis lineages. Concurrently (bottom), we sequenced metagenomic samples from all subjects and combined these reads with information obtained from isolate-defined lineages (lineage-specific SNPs) to measure lineage abundances and dynamics over time with higher sensitivity. Metagenomics also enabled analysis of species and coarse within-species diversity from subjects from which we did not perform culturing, as well as analysis from time points without cultured isolates. As we observe only modest differences between facial sites (Figure S1), consistent with prior results,18data from different facial sites were concatenated. We used metagenomics to detect transmission and turnover events and intra-lineage phylogenies (top right) to infer dynamics in further detail.
