Apis species comparison

Honeybees serve as great model for studying gut microbiota evolution in the context of host ecology and evolution given their well-documented ecology and evolutionary history. Unlike the more diverse microbiomes of humans, primates, and mice, honeybees offer a more tractable system for understanding how gut microbiota are distributed and have evolved. This research is crucial for understanding how symbiotic interactions change and evolve across species but has been hindered by the lack of high-resolution genomic data.

By leveraging shotgun metagenomics across 200 honeybees sampled from Malaysia and India, our results provide new insights into gut microbiota evolution and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.

Problem:

• Animals including humans, other primates and mice have a much more diverse microbiome with many more species making them harder to study towards understanding how gut microbiota are distributed and have evolved.
• Honeybees are a great model to study the evolution and ecology of the gut microbiome with their simple and conserved gut microbiome and well-known host ecology and evolutionary history.
• Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data.

Challenge:

• Previous studies have focused on highly diverse and variable systems, significant differences in relatedness and ecology of compared populations, geographic confounding factors, and reliance on low-resolution 16S rRNA analysis.

Expectations and Results:

• Using shotgun metagenomics on 200 honeybee workers from five species, we recovered thousands of metagenome-assembled genomes, identifying several novel bacterial species.
• We found both specialist and generalist bacteria, with notable variation between host species. Some generalists emerged host-specific only at the strain level, suggesting recent host switches.
• No evidence of codiversification was found; instead, symbiont gains, losses, and replacements led to functional differences, such as the ability to degrade pollen-derived pectin.
• This work has been released as a pre-print and is currently undergoing peer-review.