Extended Data Fig. 9: Strain- and species-level abundance of the 11 isolates in the human gut microbiome.

A total of 3,327 gut metagenome samples with at least 1 million quality-controlled reads across various data sets (HMP1-2, LLDeep, MetaHIT, 500FG, HMP2 (only the first time point was used), healthy Japanese adults, and three microbiome in cancer immunotherapy studies) were mapped to 1-kb regions in the 11 strains (filtered by 95% mapping identity). The mapped read counts were normalized to RPKM. a, Detection and abundance of the strain-specific marker regions. Median abundance across all marker regions was plotted against marker gene coverage. Points with high abundance at low coverage, for example, less than 75%, indicate limited marker region resolution and likely represent other strains of a species. b, Among the 11 strains, 4 were detected in 16 out of 3,327 microbiome samples evaluated. A strain was deemed detected if at least 95% of 1-kb regions in the marker region were detected. c, Abundance at the species level was calculated as the median abundance across all 1-kb regions in a genome using 3,327 metagenome samples with at least 1 million quality-controlled reads (mapped reads were filtered at 95% mapping identity). The mapped read counts were normalized to reads per RPKM. d, Abundance of the strain-specific marker regions in the faecal microbiome of the six healthy Japanese volunteers (donors A to F) was examined, as shown in a. A strain was deemed detected if at least 95% of the 1-kb regions in the marker region were detected. At our sequencing depth, three strains were detected in the donor B sample, and one in that of donor A. e, Abundance at the species-level was calculated as in c. The mapped read counts were normalized to RPKM.