Fig. 4

StrainGE identified previously undetected low-abundance strains in longitudinal samples from an individual with Crohn’s disease. a Stacked barplot showing the relative abundances of StrainGST calls for each of 27 longitudinal stool metagenomes from Fang et al [25]. Circles indicate the strain detected in Fang et al., colored by its StrainGST counterpart and labeled using the ST designations (ST1-ST7) assigned by Fang et al. Small gray circles indicate samples where no strain was predicted in Fang et al.; these are labeled with “n.d.” b Single-copy core phylogeny of the 14 StrainGST reference genomes with close matches to strains across samples. Colors are based on the reference’s clade; see column “Clade”. “Collapsed” column indicates which reference was selected as a representative for subsequent StrainGR analysis, when two or more references shared more than ~ 99.2% ANI. c For all sample pairs matching the same collapsed reference, the Jaccard gap similarity index and pairwise ACNI are plotted. Circles indicate comparisons where the predicted reference was the same before collapsing, and diamonds indicate cases where the predicted reference before collapsing was different. Sizes of shapes indicate the percentage of the reference genome that was callable across both strains being compared. Filled in shapes indicate whether this strain instance was undetected by MIDAS. Dark green circles are labeled with the time points compared. d Zoomed in view of the upper right corner of c)