Apis species comparison: Gut Microbiota and Host Evolution

Honeybees serve as a powerful model for studying gut microbiota evolution in the context of host ecology and evolutionary history. Unlike the highly diverse and variable microbiomes of humans, primates, or mice, honeybees harbor a small, conserved set of gut microbes shaped by well-documented ecological and evolutionary forces. This makes them a tractable system for understanding how gut microbiota are distributed and evolve across hosts.

Visual abstract of Apis microbiome study

This research is essential for advancing our understanding of microbiome interactions across species, but has been limited by a lack of high-resolution genomic data. To address this, we performed deep shotgun metagenomic sequencing on 200 honeybee workers across five Apis species, sampled from Malaysia and India.

From this dataset, we recovered thousands of metagenome-assembled genomes (MAGs), including several previously uncharacterized bacterial species. We observed both host-specialist and host-generalist bacterial lineages, with some generalists appearing host-specific only at the strain level—suggesting recent host switching events.

We found no evidence of codiversification between microbes and hosts. Instead, our results support a model of dynamic community turnover driven by symbiont gain, loss, and replacement. These changes were also reflected in functional profiles—for example, variation in genes involved in degrading pollen-derived pectin.


Key Objectives


Methodology & Highlights


Publication

This study has been released as a preprint on bioRxiv and is currently under peer review.