Fig. 3

Illustration of metagenomic contig clustering pattern and binning process. a–d VizBin-computed, k-mer signature-based scatter plots of contigs ≥ 1 kb of the low-diversity sample 6163, in which E. coli was the dominant species (91.3%, by WGS reads, same below) and multiple E. coli genomes were detected and separated. The area of each dot is proportional to the contig size. a Taxonomic assignments of contigs. Genera with relative abundance ≥ 0.2% are colored. A contig is colored if ≥ 75% of reads mapped to it were mapped to a single genus. The dashed area shows a manually selected cluster of mostly Escherichia contigs. The kernel density function of the Escherichia contigs is plotted aside, with peaks manually divided to represent genomes of multiple E. coli strains. b Contig coverage indicated by opacity. c Taxonomic assignment rate (proportion of reads mapped to the reference genome database) indicated by color depth. d Contigs with SSU(s) are highlighted. e High-diversity sample 101 from which multiple known and “dark matter” genomes were isolated. f Sample 76 featured by the presence of multiple Enterobacteriaceae genera. g Sample 540, a healthy traveler control with moderate diversity