Fig. 4

Limited strain-level diversity detected in the early pup microbiome. A Percent of nucleotide identity shared between strains of Ligilactobacillus murinus and Proteus mirabilis identified in seven shotgun-sequenced mouse samples and their most closely related NCBI genomes, L. murinus ASF361 and Proteus mirabilis swupm1, respectively, as determined by StrainGST. Sample names indicate mouse strain, litter, pup age in days, and sample number, separated by dots. B Heatmap colors indicate pairwise nucleotide identity between L. murinus strains identified in each of the seven mouse samples as determined by StrainGR. The cladogram was calculated using Euclidean distance. C Heatmap colors indicate pairwise nucleotide identity between P. mirabilis strains identified in each of the seven mouse samples as determined by StrainGR. The cladogram was calculated using Euclidean distance