Core genome phylogeny of lactobacilli. Phylogenetic tree inferred from a maximum likelihood analysis of a concatenated alignment of 303 pan-orthologous genes. Strains sequenced in the current study are highlighted in red, with their group names indicated to the right (“Firm4” and “Firm5”). The main groupings of lactobacilli as identified by Kant et al.  are indicated with bold letters. Accession numbers of all genomes are listed in Additional file 3: Table S2 (L. = Lactobacillus, Le. = Leuconostoc, W. = Weissella, O. = Oenococcus, P. = Pediococcus).