Rapid strain-specific identification of two Lactobacillus rhamnosus strains using PCR based on gene family analysis

Zhang, Chenchen; Yu, Xingtong; Wang, Dai; Gui, Yaxing; Wang, Chunlei; Wang, Jiaqi; Yin, Baoshu; Pan, Zhiming; Gu, Ruixia

doi:10.1016/j.lwt.2021.111395

Cited by 11 publications

(6 citation statements)

References 27 publications

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“…Brandt et al successfully identified L. rhamnosus GG using PCR primers based on phage Lc-Nu regions [ 35 ]. Zhang et al analyzed the genomes of L. rhamnosus LV108 and L. rhamnosus hsryfm 1301 to identify particular segments and then utilized PCR with various primers to identify the target strains at the strain level [ 36 ]. These tests need further processing of PCR products, such as gel visualization and sequencing.…”

Section: Discussionmentioning

confidence: 99%

Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus X253

Zhao

Zhang²,

Liu

et al. 2022

Foods

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Probiotics are universally recognized for their health benefits, despite the fact that their effects depend on the strain. Identification and enumeration of probiotic strains are required prior to evaluating their effectiveness. Lacticaseibacillus rhamnosus X253 is a potential probiotic strain with antioxidant capacity. Comparative genomics and single nucleotide polymorphisms (SNPs) were used to identify a strain-specific locus within the holA gene for strain X253 that was distinct in 30 different L. rhamnosus strains. Using quantitative PCR, the primers and probe designed for the locus were able to distinguish L. rhamnosus X253 from the other 20 probiotic strains. The chosen locus remained stable over 19 generations. The sensitivity of the assay was 0.2 pg genomic DNA of L. rhamnosus X253, or 103 cfu/mL bacteria of this strain. In terms of repeatability and reproducibility, relative standard deviations (RSD) were less than 1% and 3%, respectively. Additionally, this assay achieved accurate enumerations of L. rhamnosus X253 in spiked milk and complex powder samples. The strain-specific assay could be used for quality control and compliance assessment of dairy products.

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Section: Discussionmentioning

confidence: 99%

Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus X253

Zhao

Zhang²,

Liu

et al. 2022

Foods

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“…To our knowledge, the weakening effect of nitrogen sources in the growth medium on heat stress and oxidative stress tolerance has not been reported in other LABs. Interestingly, the heat stress and oxidative stress tolerance of six different L. rhamnosus strains isolated from different countries (Zhang et al 2021 ) decreased with increasing tryptone content. Therefore, this phenomenon is most likely universal for L. rhamnosus .…”

Section: Discussionmentioning

confidence: 99%

Influence of nitrogen sources on the tolerance of Lacticaseibacillus rhamnosus to heat stress and oxidative stress

Zhang

Han

Gui

et al. 2022

Journal of Industrial Microbiology and Biotechnology

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It has been found that 32 genes related to nitrogen source metabolism in Lacticaseibacillus rhamnosus are downregulated under both heat stress and oxidative stress. In this study, the influence of different nitrogen sources within the growth medium on the tolerance of L. rhamnosus to heat stress and oxidative stress was investigated. Tryptone-free MRS was found to enhance the tolerance of L. rhamnosus hsryfm 1301 to heat stress and oxidative stress during the whole growth period, and this result was universal for all L. rhamnosus species analyzed. The strongest strengthening effect occurred when the OD600 value reached 2.0, at which the survival rates under heat stress and oxidative stress increased 130 fold and 40 fold, respectively. After supplementing phenylalanine, isoleucine, glutamate, valine, histidine, or tryptophan into the tryptone-free MRS, the tolerance of L. rhamnosus to heat stress and oxidative stress exhibited a sharp drop. The spray drying survival rate of L. rhamnosus hsryfm 1301 cultured in the tryptone-free MRS rose to 75% (from 30%), and the spray dried powder also performed better in the experimentally simulated gastrointestinal digestion. These results showed that decreasing the intake of amino acids is an important mechanism for L. rhamnosus to tolerate heat stress and oxidative stress. When L. rhamnosus is cultured for spray drying, the concentration of the nitrogen source's components should be an important consideration.

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“…Probiotics exhibit strain-specific properties with regard to their safety and function [ 12 ]. It has been hypothesized that improper administration of probiotics may result in four kinds of detrimental effects: systemic infection, creation of toxic metabolites, excessive immunological activation, and transfer of antibiotic resistance and virulence genes [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Assessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis

et al. 2023

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Lacticaseibacillus rhamnosus is a generalist that can adapt to different ecological niches, serving as a valuable source of probiotics. The genome of L. rhamnosus X253 contains one chromosome and no plasmids, with a size of 2.99 Mb. Both single-copy orthologous gene-based phylogenetic analysis and average nucleotide identity indicated that dairy-derived L. rhamnosus X253 was most closely related to the human-intestine-derived strain L. rhamnosus LOCK908, rather than other dairy strains. The adaptation of L. rhamnosus X253 and the human-intestine-derived strain L. rhamnosus GG to different ecological niches was explained by structural variation analysis and COG annotation. Hemolytic assays, API ZYM assays, and antimicrobial susceptibility tests were performed to validate risk-related sequences such as virulence factors, toxin-encoding genes, and antibiotic-resistance genes in the genomes of L. rhamnosus X253 and GG. The results showed that L. rhamnosus GG was able to use L-fucose, had a higher tolerance to bile salt, and adhered better to CaCo-2 cells. In contrast, L. rhamnosus X253 was capable of utilizing D-lactose, withstood larger quantities of hydrogen peroxide, and possessed excellent antioxidant properties. This study confirmed the safety and probiotic properties of L. rhamnosus X253 via complete genome and phenotype analysis, suggesting its potential as a probiotic.

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Rapid strain-specific identification of two Lactobacillus rhamnosus strains using PCR based on gene family analysis

Cited by 11 publications

References 27 publications

Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus X253

Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus X253

Influence of nitrogen sources on the tolerance of Lacticaseibacillus rhamnosus to heat stress and oxidative stress

Assessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis

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