Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts

Abstract

The gut bacteria of honey bee recognized as a mutualistic partner with the insect host might have originated from a free-living or parasitic lifestyle. However, little is known about the genomic features underlying this lifestyle transition. Here we compared the genomes of bee gut bacteria Apibacter with their close relatives living in different lifestyles. We found that despite general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which is putatively beneficial to the host. Interestingly, the microaerobic Apibacter species specifically acquired genes encoding for the nitrate respiration (NAR). These together with nitrate transporter and enzymatic cofactor synthesis genes were found clustered in the genomes. The NAR system is also conserved in the cohabitating bee gut microbe Snodgrassella, although with a different structure. This convergence suggests a key role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation were found partially or completely lost in Apibacter. Particularly, genes encoding for the conversion to the toxic intermediates in phenylacetate degradation, as well as other potential virulence factors, are specifically lost in Apibacter group. Antibiotic resistance genes are only sporadically distributed among Apibacter species, but are prevalent in their relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advanced our knowledge of genomic features specialized to bee gut symbionts.

Impacts of Imidacloprid and Flupyradifurone Insecticides on the Gut Microbiota of Bombus terrestris

“…Apibacter are present for the de novo synthesis of all proteinogenic amino acids, except methionine, for which there is an encoded transporter [60]. Despite the general reduction in the Apibacter genome, amino acid metabolism was retained, which is putatively beneficial to the host [61]. In summary, imidacloprid exposure caused significant changes to the structure profile of the B. terrestris gut community.…”

Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected?

“…Several studies showed that environmental species, such as members of the Asaia , Apibacter , Apilactobacillus , Vagococcus , Pseudomonas , Parasaccharibacter , Citrobacter , Providencia , and Pantoea genera, often related with soil, pollen, and nectar ( 55 , 56 ), are present in the honeybee gut as minor groups ( 57 – 59 ). These non-core genera were found to increase at T1 upon treatments with SUL and TL.…”

Diet outweighs genetics in shaping gut microbiomes in Asian honeybee

“…The microbiota-free A. cerana workers were obtained following Zhang et al . [80]. Pupae in late stage were removed from brood frames and incubated in sterile plastic bins at 35 °C.…”

“…A customized bacterial genome database was constructed to enable taxonomic assignments for the bacterial assemblies. The database included all bacterial genomes available on NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/) up to Jan 2019 (167,172 genomes) , 83 genome assemblies of newly sequenced A. cerena gut bacteria (Table S2) and 14 Apibacter genomes from A. cerana [80]. Taxonomical assignments were conducted using blastn and an e-value of 1e-5.…”

“…A Gilliamella strain (B2889, belonging to the SDP Gillia_Acer_2) were cultivated with HIA, and a Lactobacillus Firm-5 strain (B4010) were cultivated with MRS with 0.02 g/ml D-frutcose (aladdin F108331) and 0.001 g/ml L-cysteine (aladdin C108238). The microbiota-free A. cerana workers were obtained following Zhang et al [80]. Pupae in late stage were removed from brood frames and incubated in sterile plastic bins at 35 °C.…”