Fig. 6

StrainGE recapitulates strain-diversity among bacterial isolates using metagenomic data only. a Single-copy core phylogenetic tree of E. faecalis isolates from the UK Baby Biome Study (UK BBS) (n = 282) in the context of isolates from other public UK hospitals (n = 168), human gut microbiota (n = 28), or other environmental sources (n = 27). Five major lineages were identified, represented by ST16, ST179, ST30, ST191, and ST40. Tree republished with permission from Shao et al. [27]. b Scatterplot relating ANI between isolates (x-axis) to StrainGE’s computed ACNI between metagenomes from which the isolates were derived (y-axis). c Barplot showing StrainGST predicted references and their relative abundances (y-axis) for strains present in metagenomic samples from a mother and her child taken over several days (x-axis). Strains matching the same reference are shown in the same color. Lines connecting bars are labeled with StrainGR computed ACNI. d For all pairs of samples with a strain close to either E. faecium DMEA02 (yellow) or E. faecalis SF28073 (blue), ACNI (y-axis) and gap similarity are plotted (x-axis). Circles with a black border represent pairs of samples from the same subject (or its mother). Size of the circle represents the percentage of common callable genome