Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis

Kang, Jahyo; Chung, Won‐Hyong; Lim, Tae-Joong; Whon, Tae Woong; Lim, Sanghyun; Nam, Young-Do

doi:10.3389/fimmu.2017.00413

Cited by 14 publications

(8 citation statements)

References 22 publications

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“…The presence of unique genes in some, but not all, L. casei strains suggests that the genome information given for the strains is incorrect. These L. casei strains were found to be more similar in the 16S rRNA gene to L. paracasei than to the L. casei described in a previous study [21]. Also, one genome of L. gallinarum contained a unique gene of L. helveticus.…”

Section: Selection Of Species-specific Sequences and Primer Designssupporting

confidence: 45%

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

et al. 2020

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Background: Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results: To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S-23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S-23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions: The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus, and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

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Section: Selection Of Species-specific Sequences and Primer Designssupporting

confidence: 45%

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

et al. 2020

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Section: Selection Of Species-specific Sequences and Primer Designssupporting

confidence: 51%

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Kim

Yang

Lim

et al. 2020

Preprint

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Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

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“…The presence/absence of core and accessory genes identified by Roary ( Supplementary Material , Data set A) additionally revealed the lower genetic relatedness of the dairy L. casei strains, ATCC393 and LC5, in relation to the others. The peculiarity of these two strains, which share a high genome similarity, has been previously highlighted (Kang et al, 2017 ). Therefore, ATCC393 and LC5 were included in the maximum-likelihood phylogenetic tree to serve as an outgroup (Figure 2 ).…”

Section: Resultsmentioning

confidence: 84%

Genetic Signatures of Dairy Lactobacillus casei Group

2018

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Lactobacillus casei/Lactobacillus paracasei group of species contains strains adapted to a wide range of environments, from dairy products to intestinal tract of animals and fermented vegetables. Understanding the gene acquisitions and losses that induced such different adaptations, implies a comparison between complete genomes, since evolutionary differences spread on the whole sequence. This study compared 12 complete genomes of L. casei/paracasei dairy-niche isolates and 7 genomes of L. casei/paracasei isolated from other habitats (i.e., corn silage, human intestine, sauerkraut, beef, congee). Phylogenetic tree construction and average nucleotide identity (ANI) metric showed a clustering of the two dairy L. casei strains ATCC393 and LC5, indicating a lower genetic relatedness in comparison to the other strains. Genomic analysis revealed a core of 313 genes shared by dairy and non-dairy Lactic Acid bacteria (LAB), within a pan-genome of 9,462 genes. Functional category analyses highlighted the evolutionary genes decay of dairy isolates, particularly considering carbohydrates and amino acids metabolisms. Specifically, dairy L. casei/paracasei strains lost the ability to metabolize myo-inositol and taurine (i.e., iol and tau gene clusters). However, gene acquisitions by dairy strains were also highlighted, mostly related to defense mechanisms and host-pathogen interactions (i.e., yueB, esaA, and sle1).This study aimed to be a preliminary investigation on dairy and non-dairy marker genes that could be further characterized for probiotics or food applications.

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Complete Genome Sequence of Lactobacillus casei LC5, a Potential Probiotics for Atopic Dermatitis

Cited by 14 publications

References 22 publications

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Genetic Signatures of Dairy Lactobacillus casei Group

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