Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function

Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 honeybee workers from five species, we recovered thousands of metagenome-assembled genomes, identifying several novel bacterial species. While microbial communities were mostly host-specific, we found both specialist and generalist bacteria, even among closely related species, with notable variation between host species. Some generalists emerged host-specific only at the strain level, suggesting recent host switches. Unexpectedly, we found no evidence of codiversification between hosts and symbionts. Instead, symbiont gains, losses, and replacements led to functional differences, such as the ability to degrade pollen-derived pectin. Our results provide new insights into gut microbiota evolution and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.