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Strain-level analysis. (a and b) Phylogenetic trees showing the relationships between E. coli strains (a) and K. pneumoniae strains (b) detected in the nunu metagenomic samples and their respective reference genomes, as predicted by StrainPhlAn. Nodes highlighted in gray indicate reference genomes of particular interest. (c) MDS showing the functional similarities between strains detected in the nunu metagenomic samples, as predicted by PanPhlAn. Reference genomes are shown in dark gray.
