The microbial gut communities of social bees comprise only a few bacterial groups and are an emerging model system to study host-associated microbial communities. In this study, Engel and colleagues used comparative metagenomics to analyse the gut microbiota of two closely related honey bee species, Apis mellifera and Apis cerana. Although they are colonized mostly by the same 16S rRNA phylotypes, the authors found that at genomic resolution, each host species harbours a highly distinct bacterial community. Compared with A. cerana, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota, encoding more diverse enzymes for polysaccharide degradation, which may provide more metabolic flexibility. Studies are now needed to understand the mechanisms and functional consequences of strain-level diversity among related host-associated communities.