Fig. 2

Core genome phylogenies of bee gut microbiota phylotypes and SDP validation. a–f The upper part of each panel shows the maximum-likelihood core genome phylogeny inferred for each of the five core phylotypes of the honey bee gut microbiota and the non-core phylotype B. apis, based on the genomes in the reference database. Different shades of color represent candidate SDPs. The lower part of each panel shows the validation of the existence of SDPs using the metagenomic data. Orthologous sequences of core genes were extracted from de novo metagenome assemblies and aligned to the core genes of the reference genomes. The two density distributions correspond to the maximum alignment percentage identity of all extracted orthologs to their highest and second-highest (grey color) scoring candidate SDP. Note that only one distribution is shown for S. alvi, since no candidate SDPs were found in the database. The total number of non-redundant orthologous sequences extracted per phylotype is indicated in the legend of the density distribution plots. Phylogenetic analyses were based on nucleotide alignments, except in the case of Firm4. Bars correspond to 0.05 substitutions per site. Published species names are placed at the leaves of the trees (for full names, see Supplementary Data 1). Names of confirmed SDPs are shown next to the internal node corresponding to their most recent common ancestor. Results for the two non-core members Commensalibacter sp. and F. perrara are shown in Supplementary Fig. 6a. Larger trees with annotations can be found in Supplementary Fig. 5