title: Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability.
abstract: We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
authors.affiliation: Research Institute, KAGOME Co., Ltd., Nasushiobara, Tochigi, Japan. Masanori_Fukao@kagome.co.jp
authors.forename: Masanori
authors.initials: M
authors.lastname: Fukao
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Morita
authors.forename: Hidehiro
authors.initials: H
authors.lastname: Toh
authors.forename: Wataru
authors.initials: W
authors.lastname: Suda
authors.forename: Seok-Won
authors.initials: SW
authors.lastname: Kim
authors.forename: Shigenori
authors.initials: S
authors.lastname: Suzuki
authors.forename: Takafumi
authors.initials: T
authors.lastname: Yakabe
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Yajima
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000235:genetics; D003227:Conjugation, Genetic / Q000235:genetics; D004270:DNA, Circular / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D042822:Genomic Instability / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D052196:Levilactobacillus brevis / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D010957:Plasmids / Q000235:genetics*; D019936:Probiotics / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004270:DNA, Circular
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