Fig. 6

Functional gene content of the gut microbiota varies across bees. a Number of gene families per phylotype assigned to the variome (gene families occurring with a relative abundance of less than 10% compared to the phylotype abundance in at least one sample). The fraction of the variome correlating in abundance with a single SDP (or phylotype, in the absence of SDPs) is indicated in dark grey shade. b COG category distribution of variome gene families. Gene families having no COG category or belonging to category S (57% of all variome gene families) were excluded from the stacked bar plots. c Frequency of occurrence of genomic islands across the sampled bees. Within each island occurrence bin, the relative fraction of gene families corresponding to major COG classes is indicated. d Genetic organization of the part of island ‘JG29_28’ (phylotype Firm4) that encodes genes for ethanolamine catabolism. e Genetic organization of island ‘Ga0133551_9 ‘ (phylotype Bifido), which encodes genes for cellulose and hemicellulose utilization. Gene colors correspond to COG categories as shown in (b). f Similarity between pairs of bees based on the shared variome, expressed as Jaccard distances with lower values indicating higher similarity. g, h Principal coordinates analysis of jaccard distances calculated from the variome, for the phylotypes Bifido (g) and Firm5 (h). Different shades of each color indicate colony origin and sampling year combination. PCoA plots for other phylotypes are shown in Supplementary Fig. 18