Genome sequencing and analysis of the first complete genome ofLactobacillus kunkeeistrain MP2, anApis melliferagut isolate

Abstract

Background.The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease ofFirmicutespopulations, such as theLactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain ofLactobacillus kunkeei(L. kunkeeistrain MP2) from the gut of Chilean honey bees.L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, theL. kunkeeigenetic background and perform a comparative genome analysis with otherLactobacillusspecies.Methods.L. kunkeeiMP2 was originally isolated from the guts of ChileanA. melliferaindividuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology.De novoassembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons betweenL. kunkeeiMP2 with otherL. kunkeei, andLactobacillusstrains were done using Roary.Results.The complete genome ofL. kunkeeiMP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16L. kunkeeistrains, identified 113 unique genes, most of them related to phage insertions. A large and unique region ofL. kunkeeiMP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with otherLactobacillusspecies, identified several unique genes ofL. kunkeeiMP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs).Discussion.The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability inL. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments.L. kunkeeicould be a new source ofLactobacilluswith beneficial properties. Indeed,L. kunkeeiMP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.