Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics

Kim, Eiseul; Yang, Seung-Min; Cho, Eun-Ji; Kim, Hae‐Yeong

doi:10.1016/j.fm.2020.103485

Cited by 38 publications

(29 citation statements)

References 31 publications

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“…We also confirmed that some genomes deposited in NCBI were misclassified. Previous studies have also reported that taxonomy information for similar species in the NCBI is incorrect (Kim et al, 2020). For Bifidobacterium, this is the first report to confirm the incorrect classification of genomes in NCBI.…”

Section: Discussionmentioning

confidence: 67%

“…Bifidobacterium strains were cultured in Bifidobacterium broth (MB cell, Seoul, South Korea) and BL broth (MB cell, Seoul, South Korea) at 37°C for 48 h under anaerobic condition. Other lactic acid bacterial strains were cultured in MRS broth (Difco, Becton Dickinson, Sparks, MD, United States) at 30°C for 48 h under anaerobic condition ( Kim et al, 2020 ). All strains were stored in 30% (v/v) glycerol (Bioshop, Burlington, ON, Canada) at −80°C until use.…”

Section: Methodsmentioning

confidence: 99%

“…7500 Real-time PCR System (Applied Biosystems, Foster City, CA, United States) and 7500 software were used for the specificity and accuracy of species-or subspecies-specific primers. (Kim et al, 2020). All strains were stored in 30% (v/v) glycerol (Bioshop, Burlington, ON, Canada) at −80 • C until use.…”

Section: Equipment and Softwarementioning

confidence: 99%

“…Species-and subspecies-specific primers were designed based on selected genetic markers using Primer Designer (Scientific and Education Software, Chapel Hill, NC, United States). All 22 primer pairs were developed to be less than 200 bp in size to increase the amplification efficiency (Kim et al, 2020) suitable for the application of processed food products. All primers were synthesized by Bionics (Seoul, South Korea).…”

Section: Comparative Genomic Analysis Of Bifidobacterium Species or Smentioning

confidence: 99%

“…To confirm the specificity of designed primers, real-time PCR was performed for 41 Bifidobacterium strains and 14 non-Bifidobacterium strains using a 7500 Real-time PCR System (Applied Biosystems, Foster City, CA, United States was obtained according to previously reported methods (Gómez-Rojo et al, 2015;Kim et al, 2020). Briefly, Bifidobacterium strains at 8 × 10 5 to 8 × 10 9 CFU/mL as determined by plate counting on Bifidobacterium agar (MB cell, Seoul, South Korea) were subjected to DNA extraction.…”

Section: Specificity and Standard Quantification Using Real-time Pcr mentioning

confidence: 99%

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Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics

Kim

Yang

et al. 2020

Front. Microbiol.

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Bifidobacterium species are used as probiotics to provide beneficial effects to humans. These effects are specific to some species or subspecies of Bifidobacterium. However, some Bifidobacterium species or subspecies are not distinguished because similarity of 16S rRNA and housekeeping gene sequences within Bifidobacterium species is very high. In this study, we developed a real-time polymerase chain reaction (PCR) assay to rapidly and accurately detect 22 Bifidobacterium species by selecting genetic markers using comparative genomic analysis. A total of 210 Bifidobacterium genome sequences were compared to select species-or subspecies-specific genetic markers. A phylogenetic tree based on pan-genomes generated clusters according to Bifidobacterium species or subspecies except that two strains were not grouped with their subspecies. Based on pan-genomes constructed, species-or subspecies-specific genetic markers were selected. The specificity of these markers was confirmed by aligning these genes against 210 genome sequences. Real-time PCR could detect 22 Bifidobacterium specifically. We constructed the criterion for quantification by standard curves. To further test the developed assay for commercial food products, we monitored 26 probiotic products and 7 dairy products. Real-time PCR results and labeling data were then compared. Most of these products (21/33, 63.6%) were consistent with their label claims. Some products labeled at species level only can be detected up to subspecies level through our developed assay.

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Section: Discussionmentioning

confidence: 67%

Section: Methodsmentioning

confidence: 99%

Section: Equipment and Softwarementioning

confidence: 99%

Section: Comparative Genomic Analysis Of Bifidobacterium Species or Smentioning

confidence: 99%

Section: Specificity and Standard Quantification Using Real-time Pcr mentioning

confidence: 99%

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Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics

Kim

Yang

et al. 2020

Front. Microbiol.

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Identification of novel molecular targets for Weissella species-specific real-time PCR based on pangenome analysis

Kim

Yang

Kim

et al. 2022

Appl Microbiol Biotechnol

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Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes

Hong,

Yang,

Kim

et al. 2023

Appl Microbiol Biotechnol

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Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics

Cited by 38 publications

References 31 publications

Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics

Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics

Identification of novel molecular targets for Weissella species-specific real-time PCR based on pangenome analysis

Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes

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