Figure 2. Whole genome MLST analysis of the infraspecies diversity of L. acidophilus.

A Neighbor Net plot was generated using wgMLST. The scale bar indicates distance measured in number of allelic differences over 1815 genomic loci conserved across all L. acidophilus genomes examined. Isolate numbers are coloured to represent their commercial (blue) or culture collection (green) history (Table 1), with other notable groups circled. High resolution analysis of the 14 commercial L. acidophilus genome sequences in the circled region of the neighbour net plot is provided in Supplementary Figure S1. The NFCM isolate genome sequenced as part of this study is indicated by an asterisk. The GenBank accession of the NCFM reference genome sequence is given brackets. Numbers given in superscript indicate CRISPR sequence types assigned in Supplementary Figure S2.