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. 2021 Aug 6;16(2):388–399. doi: 10.1038/s41396-021-01071-0

Fig. 3. Strain-level diversity of S. thermophilus in cheese starter cultures.

Fig. 3

A Alternative allele frequencies of all S. thermophilus SNVs over the metagenomic samples. Recurring SNVs from different samples are connected with a line. Clustering of lines indicates a large amount of SNVs with similar frequencies suggesting genomic coupling. Sample labels on the x-axis correspond to samples highlighted in Fig. 2A. B The phylogeny of the isolated S. thermophilus strains based on maximum likelihood analysis on 1788 core genes. The isolates split into four lineages indicated by different color shadings. Strains sequenced with Nanopore are labelled with an asterisk. Values on branches indicate bootstrap values (100 replicates). C The relative abundance of each of the four sub-lineages of S. thermophilus across the 11 metagenomes as based on the average frequency of lineage-specific SNVs identified on the basis of the isolates in Fig. 3B.