Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers

Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities shift in strain composition in response to environmental changes has mostly remained elusive. Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of Western honeybees, larvae-feeding nurses and pollen foragers. While their gut microbiota is composed of the same bacterial species, we detected consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species clustered by behavioral state rather than by colony or sampling location. Moreover, we identified strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states. Our findings show that strain-level diversity in host-associated communities can turnover in response to environmental changes modulating functional traits of communities and highlighting that strains are ecologically relevant units.