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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 of  Firmicutes  populations, such as the  Lactobacilli . At this time, the causes of these alterations remain unknown. We recently isolated a strain of  Lactobacillus kunkeei  ( L. kunkeei  strain 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, the  L. kunkeei  genetic background and perform a comparative genome analysis with other  Lactobacillus  species.   Methods.   L. kunkeei  MP2 was originally isolated from the guts of Chilean  A. mellifera  individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology.  De novo  assembly 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 between  L. kunkeei  MP2 with other  L. kunkeei , and  Lactobacillus  strains were done using Roary.   Results.  The complete genome of  L. kunkeei  MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16  L. kunkeei  strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of  L. kunkeei  MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other  Lactobacillus  species, identified several unique genes of  L. kunkeei  MP2 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 in  L. 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. kunkeei  could be a new source of  Lactobacillus  with beneficial properties. Indeed,  L. kunkeei  MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.

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