Fig. 2

Metagenomic read mapping delineates gut pathogen colonization at high abundance in EBI cases. A Genome breadth of coverage (filtered by ≥ 0.5 for visualization) and popANI of pairwise metagenomic read mapping to EBI pathogens. Each dot represents an individual alignment, and colors correspond to whether the metagenome mapped to a genome from the same infant and whether that pathogen had been cultured from the gut (“culture match”). Dot size is scaled to read depth-normalized coverage. Dashed line indicates the minimum popANI (99.999%) that was determined to be specific to within-infant alignments. B Relative abundance of the EBI-causing species compared to normalized coverage for within-infant mappings of metagenomic reads to pathogen genomes for strains determined to be present in the gut via culturing and/or inStrain (as indicated by color). Dashed line indicates the minimum relative abundance (1%) of the pathogen species that enabled metagenomic detection of the EBI-causing strain. Dot size is scaled to popANI. Pearson correlation coefficient (R) and p value are shown