Museum-omics opens a new avenue for investigating honey bee host-microbiome coevolution

As critical pollinators, honey bees possess gut microbiotas that are socially transmitted across generations, forming tight symbiotic interactions and coevolving with their hosts. These relationships are indispensable for tracing evolutionary histories and understanding adaptive mechanisms to environmental changes from a phylogenomic perspective.

However, methodologies and the feasibility of simultaneously retrieving genetic information for both the host and its gut microbes from historical specimens have not yet been reported. Here, we performed DNA extraction on 16 historical Apis cerana specimens (1955–1988) to compare traditional hindleg extractions with abdominal gut tissue extractions. We systematically evaluated DNA quantity, degradation, damage patterns, and endogenous mapping rates for both host and core gut bacteria.