Core genome phylogeny of bifidobacterial strains. Phylogenetic tree inferred from a maximum likelihood analysis of a concatenated alignment of 400 pan-orthologous genes. Strains sequenced in the current study are highlighted in red, with their group names indicated to the right (“Bifido-1” and “Bifido-2”). Other strains isolated from the honeybee gut are shown in light blue, and strains isolated from the bumblebee gut are shown in dark blue. Accession numbers of all genomes are listed in Additional file 3: Table S2.