Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability

Masanori Fukao, Kenshiro Oshima, Hidetoshi Morita, Hidehiro Toh, Wataru Suda, Seok Won Kim, Shigenori Suzuki, Takafumi Yakabe, Masahira Hattori, Nobuhiro Yajima

Research output: Contribution to journalArticle

30 Citations (Scopus)

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.

Original languageEnglish
Article numbere60521
JournalPLoS One
Volume8
Issue number3
DOIs
Publication statusPublished - 2013 Mar 27
Externally publishedYes

Fingerprint

Lactobacillus brevis
High-Throughput Nucleotide Sequencing
Genomic Instability
Probiotics
probiotics
plasmids
Plasmids
Genes
genomics
Genome
Bacteria
genome
Chromosomes, Human, Pair 2
genes
Virulence Factors
plasmid curing
Vegetables
Cell Wall
Polysaccharides
Gastrointestinal Tract

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability. / Fukao, Masanori; Oshima, Kenshiro; Morita, Hidetoshi; Toh, Hidehiro; Suda, Wataru; Kim, Seok Won; Suzuki, Shigenori; Yakabe, Takafumi; Hattori, Masahira; Yajima, Nobuhiro.

In: PLoS One, Vol. 8, No. 3, e60521, 27.03.2013.

Research output: Contribution to journalArticle

Fukao, M, Oshima, K, Morita, H, Toh, H, Suda, W, Kim, SW, Suzuki, S, Yakabe, T, Hattori, M & Yajima, N 2013, 'Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability', PLoS One, vol. 8, no. 3, e60521. https://doi.org/10.1371/journal.pone.0060521
Fukao, Masanori ; Oshima, Kenshiro ; Morita, Hidetoshi ; Toh, Hidehiro ; Suda, Wataru ; Kim, Seok Won ; Suzuki, Shigenori ; Yakabe, Takafumi ; Hattori, Masahira ; Yajima, Nobuhiro. / Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability. In: PLoS One. 2013 ; Vol. 8, No. 3.
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