The symbiotic bacteria associated with honeybee gut have likely
transformed from a free-living or parasitic lifestyle, through a close
evolutionary association with the insect host. However, little is known
about the genomic mechanism underlying bacterial transition to exclusive
adaptation to the bee gut. Here we compared the genomes of bee gut
symbionts Apibacter with their close relatives living in different
lifestyles. We found that despite of general reduction in the Apibacter
genome, genes involved in amino acid synthesis and monosaccharide
detoxification were retained, which was likely beneficial to the host.
Interestingly, the microaerobic Apibacter species have specifically
preserved the NAR operon encoding for the nitrate respiration pathway
which in contrast, is absent from the related non-free-living
microaerobic pathogenic relatives. The NAR operon is also conserved in
the cohabiting bee microbe Snodgrasella, but with a differed structure.
This convergence implies a crucial role of respiration nitrate reduction
for microaerophilic microbiomes to colonize bee gut epithelium. Genes
involved in lipid, histidine and phenylacetate degradation are partially
lost in Apibacter, possibly associated with the loss of pathogenicity.
Antibiotic resistance genes were only sporadically distributed among
Apibacter species, but condensed in their pathogenic relatives.
Collectively, this study advanced our understanding of genomic
transition underlying specialization in bee gut symbionts.