Fig. 2: micov detects phenotypically relevant strain variation, captures changes in genome abundance at the level of a single genomic copy in wastewater, and exhibits sensitive detection in low-biomass specimens.

a A scaled position plot of P. copri in human gut microbiome samples collected from subjects in the US/UK/Mexico stratified by presence/absence of region PC351. Sample groups are ordered by increasing sample size. Grey dotted gridlines are added as a visual esthetic to help understand the data relationship to the genome coordinates on the y-axis; b Coverage presence in this region is associated with greater overall genome coverage, with supporting Kolmogorov-Smirnov statistics. Notably, overall coverage was not significantly different between the US and UK for individuals containing the region (KS test, stat=0.17, p = 0.0711), nor was it if they both lacked the region (KS test, stat=0.12, p = 0.0434; n.s. if corrected); c Common high effect size variables, and per-sample characterization of region presence/absence, were tested with PERMANOVA against Weighted UniFrac;PCoAs of the weighted UniFrac distances colored by the region (d) and colored by country (e); f A receiver operator curve for a nested cross validated Random Forest classifier predicting presence/absence of PC351; g Coverage for region L682 in the Lachnospiraceae genome exhibiting differential coverage related to the diversity of plant consumption; h Detection of enteropathogenic E. coli (EPEC) at increasing levels of genome copies spiked into untreated wastewater (Methods). All spike-in levels show statistically significant elevated cumulative coverage levels compared to the background. A low background amount of E. coli is expected in wastewater. Only samples with non-zero EPEC coverage coverage (n = 562) are shown; i The cumulative coverage of M. gnavus from different tissue types surgically collected from Crohn’s Disease patients; j with supporting Kolmogorov-Smirnov statistics. The set of statistics shown are those which reported an uncorrected p-value below 0.05, with correction by the Bonferroni procedure; asterisks denote corrected p-values below 0.05. All Kolmogorov-Smirnov and PERMANOVA tests are in Supplementary Table 2.