Fig. 2

Sensitivity and specificity comparison to other strain prediction tools. A SameStr detects dominant and subdominant strains at low sequencing depth (mean-fold target strain coverage) and relative abundance (i.e., high noise coverage) in simulated metagenomes (n = 3276) of multi-strain species populations, compared to consensus variant profile similarity (CVS)-based methods. B Using MetaPhlAn’s clade-specific marker gene database (db_v20), SameStr identifies more genera and species per metagenomic sample (n = 65) than StrainFinder, which uses mg-OTUs that are defined based on phylogenetic comparisons of universally distributed bacterial genes from the AMPHORA database. C Fewer shared strain calls demonstrate the increased specificity of SameStr compared to StrainFinder, which allows for the differentiation of related (n=555) and unrelated (n=1,525) sample pairs. D Cumulative relative abundance and fraction of species for which strain-level resolution was achieved with SameStr in fecal metagenomes from a reference cohort of 67 longitudinally sampled healthy adults (n = 202). E SameStr’s MVS-based method detects shared strains in a larger fraction of species in related (same individual, n = 281) but not in unrelated (different individuals, n = 20,020) sample pairs of the control cohort (n = 202 individuals) compared to CVS-based methods