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 microaerobicApibacter 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.