Gut microbiome of wild and managed honeybees

Little is known about the gut microbiome of wild honeybees. Taking advantage of a large collection of wild honeybees of various subspecies from across Africa, painstakingly put together by our collaborators, we are investigating the differences in the gut microbiome of wild and managed honeybees. We are using shotgun metagenomics to resolve strain-level differences in the gut bacterial community and are currently analyzing the data to identify bacterial strains and species that are found in wild and managed honeybees and investigating their distribution across colonies of different subspecies.

Context

• In Europe and North America, nearly all honeybees are managed or feral populations derived from managed stock
• Truly wild honeybee populations are now mostly restricted to parts of Africa and Asia, where they occur in native habitats and show rich subspecies-level diversity
• With their simple and specialized gut microbiomes, honeybees serve as a powerful model to investigate how domestication and management affect microbial evolution

Challenge

• Assembling a global wild bee collection is logistically complex—thanks to an extensive international network of collaborators across Africa, and expert field ecologists in Germany, we now have hundreds of samples from genetically distinct wild colonies
• The differences we seek are expected to be subtle and strain-specific, requiring deep shotgun metagenomic sequencing and modern bioinformatics pipelines to achieve the necessary resolution

Expectations and Preliminary Results

• We have identified species-level bacterial patterns shared between wild and managed bees
• We observed lear patterns of strain-level variation across managed colonies and subspecies
• From our previous work we expected that the strain-level differences in the gut microbiome will reflect the evolutionary history of the honeybee subspecies. However, early results suggest that the differences are driven by whether the colonies are managed or wild, rather than by subspecies.