Fig. 6

Binning of the shotgun metagenomic data and reconstruction of the genomes. a Scatterplot representing the distribution of the assembled contigs based on their GC content and abundance. b Phylogenetic tree of the draft genomes (bins, n = 24) from the MAGs (metagenome assembled genomes) data (completeness > 70%, contamination < 10%). The tree was produced from concatenated alignments of up to 400 ubiquitously conserved proteins identified with PhyloPhlAn and used the SGB (species-level genome bins) release to assign to each genome bin its closest SGB. Genome bin 3, 5, 11, 13, and 19 were confidently assigned to the Sphingomonas genus using a higher-resolution phylogenetic tree (Additional file 1: Fig. S4). c The abundance (genome copies per million reads) of the Sphingomonas bins in the infected and uninfected samples