FIG 4.

Phylogenetic relationship among detected Salmonella enterica serotype Typhimurium strains from fecal metagenomes of mice. A maximum likelihood tree shows the phylogenetic distance among the Salmonella strains serotyped from stool metagenomes of mice before and after oral infection. Raw reads from each metagenome were mapped to the genome (GenBank accession number CP001363) of the infection strain (str. 14028s), high-quality single nucleotide polymorphisms (SNPs) were identified, and a core genome SNP maximum likelihood tree was built using methods similar to those previously described in reference 36.