Comparative Genome Analysis of Lactobacillus plantarum GB-LP3 Provides Candidates of Survival-Related Genetic Factors
Abstract
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced. Comparative genome analysis of GB-LP3, with other 14 L. plantarum strains, was conducted. In addition, genomic island regions were investigated. The assembled whole GB-LP3 genome contained a single circular chromosome of 3,206,111bp with the GC content of 44.7%. In the phylogenetic tree analysis, GB-LP3 was in the closest distance from ZJ316. The genomes of GB-LP3 and ZJ316 have the high level of synteny. Functional genes that are related to prophage, bacteriocin, and quorum sensing were found through comparative genomic analysis with ZJ316 and investigation of genomic islands. dN/dS analysis identified that the gene coding for phosphonate ABC transporter ATP-binding protein is evolutionarily accelerated in GB-LP3. Our study found that potential candidate genes that are affected by environmental adaptation in Korea traditional fermented vegetable.
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Strain 55A formed a different cluster than 54B and 54C and displayed a high degree of similarity with L. plantarum LP3, which was originally isolated from vegetables.
“The strain 55A formed a different cluster than the 54B and 54C and displayed a high degree of similarity with the strain L. plantarum LP3, which was originally isolated from vegetables [36].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [36]
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- Authors
- Jeon, S., Jung, J., Kim, K., Yoo, D., Lee, C., Kang, J., Cho, K., Kang, D.-K., Kwak, W., Yoon, S. H., Kim, H., & Cho, S.
- Affiliations
- Seoul National University (KR)
- Dankook University (KR)
- Corresponding author
- Cho, Seoae
- ORCID
- Venue
- Infection Genetics and Evolution
- Publisher
- Elsevier BV
- Published
- 2017-09
- Volume
- 53
- Pages
- 218-226
- ISSN
- 1567-1348 (ISSN-L)
- OpenAlex
- W2616397171
- Cited by
- 7
- References
- 43
- Citations by year
- 2026: 1 · 2024: 2 · 2023: 1 · 2022: 1 · 2020: 1 · 2018: 1
- FWCI
- 0.62
- Type
- journal article
- Language
- en
- Update notices
- erratum (2018-04-01)
- Open access
- closed
- Locations
- Infection Genetics and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Next-Generation BioGreen 21 Program (PJ011115901)
- Rural Development Administration
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Lactobacillus plantarum, comparative genomics, genomic islands, environmental adaptation, fermented vegetables, prophages, bacteriocins, quorum sensing, dN/dS, synteny, phylogenetic analysis, survival-related genes
- MeSH terms
- Whole Genome Sequencing, Animals, Bacterial Proteins, Bacteriocins, Base Composition, Chromosomes, Bacterial, Fermentation, Phylogeny, Vegetables, Gene Expression, Genome, Bacterial, ATP-Binding Cassette Transporters, Prophages, Genomic Islands, Lactobacillus plantarum, Lactiplantibacillus plantarum, Microbial Viability, Quorum Sensing
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