Fig. 1

Levels of concordance with the species phylogeny for core genes sorted from lowest (left) to highest (right) for the 16S rRNA gene hypervariable regions (16S HVR, purple), rRNA genes (rRNA, pink), coding ribosomal genes (CR, light blue), non-ribosomal genes (NR, dark blue), and rpo genes (rpo, green). Colored dots correspond to levels of concordance with the species phylogeny for genes (and hypervariable regions). Degree of shading represents the number of loci observed for each level of concordance. For 16S HVR, SC, and NR, a single dot for each genus contains a number that shows the maximum number of loci observed across all levels of concordance for that genus. This dot will have the darkest level of shading. In all cases, there are multiple dots with this maximum level of shading and maximum loci count. For rRNA and rpo, there are only three loci (5S, 16S, 23S and rpoA, rpoB, rpoC) each with a frequency of one and the same degree of shading. The following designations indicate average concordance for each genus: Staphylococcus (S), Legionella (L), Clostridium (Cl), and Campylobacter (Ca). Hypervariable regions frequently used in microbiome research (V3-V4) are highlighted. Individual rRNA and rpo genes are designated as follows: 16S rRNA gene (16S), 23S rRNA gene (23S), 5S rRNA gene (5S), rpoA gene (A), rpoB gene (B), and rpoC gene (C)