Fig. 4

Functional profiling of the species of the MetaSUB dataset across the New York urban environment. a PanPhlAn presence-absence matrix of Escherichia coli. The rows represent the gene families while columns represent the samples. The top colorbar highlights the New York Borough and the E. coli reference genomes’ phylogroups. In the heatmap yellow corresponds to presence, black corresponds to absence. Only the gene-families present in less than 90% and more than 10% of the samples were included. b PCA plot based on the genetic distance computed on the species-specific markers sequences of 416 samples and 18 reference genomes of Pseudomonas stutzeri as reported in Fig. 2c. Each point is a sample and is colored according to the presence-absence of the mexA component of the Pseudomonas MexAB-OprM efflux system