Extended Data Fig. 2: Representative isolates capture the S. epidermidis lineage diversity of individuals and families.

In a previous study, up to 96 isolates of S. epidermidis were cultured from each of 23 participants at each timepoint sampled during a 1.5-year time period. Six families were selected for inclusion in this study. Relative lineage abundance, as determined from isolates, is plotted for each sample, organized by participant and family. PHLAME was applied to metagenomic samples from the same participant (denoted as MG), which confirmed that lineage abundances estimated by culturing did not have significant culture bias; note that uncalled portions of metagenomic samples (space above bars) can reflect uncertainty in PHLAME due low coverage rather than the true absence of lineages. We used isolate-based lineage abundances because deep metagenomic coverage of S. epidermidis was not available for every sample. Sample labels indicate the family, participant, and sampling timepoint (for example 1AA3 indicates Family 1, participant 1AA, timepoint 3). The number of S. epidermidis colonies isolated from each person is indicated above each bar. Lineages represented in the TSA antagonism screen in this study are indicated in color, while unrepresented lineages are indicated in greyscale. Some additional lineages were included in a follow-up screen M9 + S screen (see Methods); these are indicated by darker grey colors (denoted by *). Colors do not carry over across families, lineages are generally restricted to a family. Across all samples, the average proportion of lineage composition represented by isolates included in the TSA antagonism screen was 96%. Participant 8PB reported antibiotic use between timepoints, which may explain the difference between timepoints.