Differentiation of lactic acid bacteria based on RFLP analysis of the tuf gene

Park, Seok-Hwee; Jung, Jong‐Hyun; Seo, Dong-Ho; Lee, Hye-Lim; Kim, Gye-Won; Park, Sunyoung; Shin, Woo-Chang; Hong, Sungyoul; Park, Cheon-Seok

doi:10.1007/s10068-012-0119-9

Cited by 6 publications

(10 citation statements)

References 28 publications

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“…On the other hand, it was not possible to obtain results which would enable the differentiation of two sub-species of L. paracasei ( Figure S2B). The observations made confirm earlier reports that RFLP is an effective and very reproducible method that enables identification of bacteria, mainly at the species level [13,29].…”

Section: Genus Species and Subspecies-specific Pcrsupporting

confidence: 88%

“…The obtained amplicons, each approximately 995 bp in length, were digested with the ApoI enzyme (5'-RˆAATTY-3'), and the digest products were separated in agarose gel. As in the study by Park et al [29], characteristic species-specific restriction profiles were observed for L. casei, L. paracasei and L. rhamnosus species. The results obtained were characterized by high reproducibility, confirmed by DNA profiles obtained for all 30 strains ( Figure S2).…”

Section: Genus Species and Subspecies-specific Pcrsupporting

confidence: 76%

“…In the case of the PCR products obtained for the tuf gene (800 bp), an enzyme recognizing the four-nucleotide sequence 5'-GGˆCC-3'-HaeIII was used for restriction digestion [16,29]. Although, in comparison to ARDRA, a smaller number of bands was obtained, different DNA profiles were obtained for all the examined species ( Figure 1).…”

Section: Genus Species and Subspecies-specific Pcrmentioning

confidence: 99%

“…In the final experimental system tested, the dnaK gene, encoding the 70-kDa heat shock protein (HSP70), which is considered a very useful genetic marker in bacterial phylogenetics studies, was replicated [23,30]. A bioinformatics analysis showed an average variation of 87.8% in dnaK sequences among type strains of species belonging to the L.casei group, which, compared to 99.1% variation in the 16S rRNA genes, seems to predispose this gene for use in the RFLP procedure [29]. The obtained amplicons, each approximately 995 bp in length, were digested with the ApoI enzyme (5'-RˆAATTY-3'), and the digest products were separated in agarose gel.…”

Section: Genus Species and Subspecies-specific Pcrmentioning

confidence: 99%

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Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

Jarocki

Komoń-Janczara

Glibowska

et al. 2020

IJMS

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The genus Lactobacillus includes, among others, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus, species that are collectively referred to as the Lactobacillus casei group. Many studies have shown that strains belonging to this group may decrease lactose intolerance, the effects of inflammatory bowel disease, diarrhea, constipation, food allergies and even colon cancer. Moreover, evidences exists of positive effects of these bacteria on mucosal immunity and blood cholesterol level. Because of their beneficial influence on human health, many of them are used as food additives and probiotic pharmaceuticals. It should be stressed that health-promoting properties are not attributed at the species level, but to specific strains. Therefore, procedures are necessary to allow specific identification at each phylogenetic level—genus, species and strain. In this paper we present a practical overview of molecular methods for the identification and differentiation of L. casei bacteria. The research included 30 bacterial strains belonging to three species: L.casei, L. paracasei and L. rhamnosus. Among the tested procedures were genus- and species-specific PCR, multiplex-PCR, Real-Time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting. The obtained results showed that multiplex-PCR and MALDI-TOF MS turned out to be the most useful methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power. We hope that the presented results will allow for the easy selection of an appropriate procedure, depending on the experiment conducted and the equipment capabilities of any given laboratory.

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Section: Genus Species and Subspecies-specific Pcrsupporting

confidence: 88%

Section: Genus Species and Subspecies-specific Pcrsupporting

confidence: 76%

Section: Genus Species and Subspecies-specific Pcrmentioning

confidence: 99%

Section: Genus Species and Subspecies-specific Pcrmentioning

confidence: 99%

See 2 more Smart Citations

Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

Jarocki

Komoń-Janczara

Glibowska

et al. 2020

IJMS

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“…All the genes mentioned above have also been used to differentiate other bacterial species. Lactic acid bacteria have been differentiated and identified using RFLP analysis of rpoB (Claisse et al , 2007), 16S rRNA/16S-23S rRNA intergenic spacer region (Ruiz et al , 2000), and tuf (Park et al , 2012). Moreover, partial cpn60 gene sequences (500 to 550 bp), have been useful to identify novel species such as Lactobacillus selangorensis (Haakensen et al , 2011), Sphingobacterium detergens (Marqués et al , 2012); Methylobacterium gnaphalii (Tani et al , 2012), and Prevotella jejuni (Hedberg et al , 2013), among many others.…”

mentioning

confidence: 99%

Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences

Pérez‐López

Olivier

Luna-Rodríguez

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Phytoplasmas are unculturable, phytopathogenic bacteria that cause economic losses worldwide. As unculturable micro-organisms, phytoplasma taxonomy has been based on the use of the 16S rRNA-encoding gene to establish 16Sr groups and subgroups based on the restriction fragment length polymorphism (RFLP) pattern resulting from the digestion of amplicon (in vitro) or sequence (in silico) with seventeen restriction enzymes. Problems such as heterogeneity of the ribosomal operon and the inability to differentiate closely related phytoplasma strains has motivated the search for additional markers capable of providing finer differentiation of phytoplasma strains. In this study we developed and validated a scheme to classify phytoplasmas based on the use of cpn60 universal target (cpn60 UT) sequences. Ninety-six cpn60 UT sequences from strains belonging to 19 16Sr subgroups were subjected to in silico RFLP using pDRAW32 software, resulting in 25 distinctive RFLP profiles. Based on these results we delineated cpn60 UT groups and subgroups, and established a threshold similarity coefficient for groups and subgroups classifying all the strains analysed in this study. The nucleotide identity among the reference strains, the correspondence between in vitro and in silico RFLP, and the phylogenetic relationships of phytoplasma strains based on cpn60 UT sequences are also discussed.

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Tracking of deliberately inoculated Leuconostoc mesenteroides and Lactobacillus brevis in kimchi

Sharma

Kaur

Lee

2019

Food Sci Biotechnol

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Differentiation of lactic acid bacteria based on RFLP analysis of the tuf gene

Cited by 6 publications

References 28 publications

Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level

Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences

Tracking of deliberately inoculated Leuconostoc mesenteroides and Lactobacillus brevis in kimchi

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