CSI phylogeny.

The single nucleotide polymorphism (SNP)-based CSI phylogeny Web application (https://cge.cbs.dtu.dk/services/CSIPhylogeny) was applied with default settings for species identification. In short, CSI phylogeny maps each contig against a chosen reference genome using BWA v. 0.7.2 (20). Afterwards, SNPs are called using SAMtools v. 0.1.18 (21), leaving out all SNPs in a 10-base vicinity of each other. CSI phylogeny returns a newick file for tree visualization. All strains were tested using their full assembled genomes, and sequences were uploaded in a fasta format (16). To avoid any bias toward a single species used in this study, we used Streptococcus sanguinis ATCC 10556^T as the reference genome.