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

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 19...

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Main Authors:	Fukao, Masanori, Oshima, Kenshiro, Morita, Hidetoshi, Toh, Hidehiro, Suda, Wataru, Kim, Seok-Won, Suzuki, Shigenori, Yakabe, Takafumi, Hattori, Masahira, Yajima, Nobuhiro
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609814/

id	pubmed-3609814
recordtype	oai_dc
spelling	pubmed-36098142013-03-29 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 Research Article 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. Public Library of Science 2013-03-27 /pmc/articles/PMC3609814/ /pubmed/23544154 http://dx.doi.org/10.1371/journal.pone.0060521 Text en © 2013 Fukao et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Fukao, Masanori Oshima, Kenshiro Morita, Hidetoshi Toh, Hidehiro Suda, Wataru Kim, Seok-Won Suzuki, Shigenori Yakabe, Takafumi Hattori, Masahira Yajima, Nobuhiro
spellingShingle	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
author_facet	Fukao, Masanori Oshima, Kenshiro Morita, Hidetoshi Toh, Hidehiro Suda, Wataru Kim, Seok-Won Suzuki, Shigenori Yakabe, Takafumi Hattori, Masahira Yajima, Nobuhiro
author_sort	Fukao, Masanori
title	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability
title_short	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability
title_full	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability
title_fullStr	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability
title_full_unstemmed	Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability
title_sort	genomic analysis by deep sequencing of the probiotic lactobacillus brevis kb290 harboring nine plasmids reveals genomic stability
description	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.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609814/
_version_	1611965763803938816

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

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