Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate
Journal
PeerJ
ISSN
2167-8359
Date Issued
2016
Author(s)
Brad Miller
Lauren A. Marks
Jonathan M. Koller
Blake J. Newman
G. Larry Bretthorst
Kevin J. Black
JUAN ANTONIO UGALDE CASANOVA
Type
Resource Types::text::journal::journal article
URL Institutional Repository
Abstract
<jats:p><jats:bold>Background.</jats:bold>The honey bee (<jats:italic>Apis mellifera</jats:italic>) 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<jats:italic>Firmicutes</jats:italic>populations, such as the<jats:italic>Lactobacilli</jats:italic>. At this time, the causes of these alterations remain unknown. We recently isolated a strain of<jats:italic>Lactobacillus kunkeei</jats:italic>(<jats:italic>L. kunkeei</jats:italic>strain MP2) from the gut of Chilean honey bees.<jats:italic>L. kunkeei</jats:italic>, 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<jats:italic>L. kunkeei</jats:italic>genetic background and perform a comparative genome analysis with other<jats:italic>Lactobacillus</jats:italic>species.</jats:p><jats:p><jats:bold>Methods.</jats:bold><jats:italic>L. kunkeei</jats:italic>MP2 was originally isolated from the guts of Chilean<jats:italic>A. mellifera</jats:italic>individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology.<jats:italic>De novo</jats:italic>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<jats:italic>L. kunkeei</jats:italic>MP2 with other<jats:italic>L. kunkeei</jats:italic>, and<jats:italic>Lactobacillus</jats:italic>strains were done using Roary.</jats:p><jats:p><jats:bold>Results.</jats:bold>The complete genome of<jats:italic>L. kunkeei</jats:italic>MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16<jats:italic>L. kunkeei</jats:italic>strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of<jats:italic>L. kunkeei</jats:italic>MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other<jats:italic>Lactobacillus</jats:italic>species, identified several unique genes of<jats:italic>L. kunkeei</jats:italic>MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs).</jats:p><jats:p><jats:bold>Discussion.</jats:bold>The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in<jats:italic>L. kunkeei</jats:italic>. 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.<jats:italic>L. kunkeei</jats:italic>could be a new source of<jats:italic>Lactobacillus</jats:italic>with beneficial properties. Indeed,<jats:italic>L. kunkeei</jats:italic>MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.</jats:p>
Subjects
lactobacillus
;
comparative genomics
;
apis mellifera
;
honeybee