A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont

Abstract

Background To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis. Results The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont. Conclusion The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.

Commensalibacter nepenthis sp. nov. and Commensalibacter oyaizuii sp. nov., from fluid in a Nepenthes pitcher cup and a butterfly (Junonia lemonias) in Thailand

“…The presence of a correlation between the two samples indicated that just Nepenthes gracilis exhibits insectivorous behaviour, hence implying the potential presence of insect-related chemicals in its fluid. However, it is important to note that the statement presented here is just our hypothesis [3, 8, 14, 16].…”

“…An analysis of the completeness of kegg metabolic pathways revealed a species-specific occurrence and degree of completeness of various metabolic pathways (). The results obtained demonstrated that Commensalibacter species had similar genetic potential in relation to carbohydrate metabolism but showed significant differences in their amino acid metabolism [8]. When compared to other species of the genus Commensalibacter , strain TBRC 10068 T contains the genome that encodes a pathway for histidine degradation to glutamate (M00045) but lacked the genomes for dissimilatory nitrate reduction (M00530) and molybdenum cofactor biosynthesis (M00880).…”

“…Several studies have been undertaken to examine the correlation between Commensalibacter strains and the overall health of their respective insect hosts. However, current knowledge of the taxonomic and functional diversity of Commensalibacter isolates among different insect hosts, as well as the level of coherence within the genus, remains unclear [3,8,13,14,16,[18][19][20].…”

Proposal of three novel insect-associated Commensalibacter species: Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov.

“…Detailed species descriptions are not part of the scope of most non-taxonomic journals, and therefore the possibility of publishing species descriptions in supplementary material of non-taxonomic journals would have opened the field of taxonomy to a broader microbiology audience. Below we provide descriptions of three novel Commensalibacter species published earlier as part of supplementary information of a paper in a journal targeting an audience of animal microbiome researchers [1] for the sole purpose of allowing the validation of their names. All taxonomic analyses and methods used to delineate the three novel species were presented earlier [1].…”

“…Below we provide descriptions of three novel Commensalibacter species published earlier as part of supplementary information of a paper in a journal targeting an audience of animal microbiome researchers [1] for the sole purpose of allowing the validation of their names. All taxonomic analyses and methods used to delineate the three novel species were presented earlier [1].…”