Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium

Sidarenka, A. V.; Новик, Г. И.; Акимов, В. Н.

doi:10.1134/s0026261708030016

Cited by 13 publications

(10 citation statements)

References 55 publications

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“…At present it is accepted by taxonomists that a similarity score for 16S rDNA falling between 97 and 99% is sufficient for identification of bacteria to genus and species levels respectively 13. Nevertheless, in the case of closely related species, even the full sequence of 16S rDNA is insufficient for differentiation, because the interspecies level of 16S rRNA gene similarity varies within the range 93–99 % 7. In the ‘ L. casei group’, identities can reach more than 99% for distinct species, which makes discrimination problematic.…”

Section: Discussionmentioning

confidence: 99%

“…The ARDRA technique is a powerful tool for identification of bifidobacteria and lactobacilli in general 4–7. AluI, HhaI, MseI and RsaI are commonly used enzymes in restriction profile analysis 14, 15.…”

Section: Discussionmentioning

confidence: 99%

“…The majority of molecular identification methods are based on the analysis of 16S rDNA. Amplified ribosomal DNA restriction analysis (ARDRA) has been widely used for the differentiation of microbes and has proved its usefulness in the identification of Bifidobacterium and Lactobacillus strains 4–7. This technique is based on amplification of the 16S rDNA region followed by digestion of the polymerase chain reaction (PCR) product with one or more restriction enzymes 8.…”

Section: Introductionmentioning

confidence: 99%

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Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria

et al. 2012

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria

et al. 2012

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“…These fingerprinting methods have the disadvantage of a low reproducibility, and they need strict standardization of PCR conditions. The use of different polymerases, DNA/primer ratios or different annealing temperatures may lead to a discrepancy in the results obtained in different laboratories [24]. …”

Section: Introductionmentioning

confidence: 99%

Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment

et al. 2013

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BackgroundBifidobacterium represents one of the largest genus within the Actinobacteria, and includes at present 32 species. These species share a high sequence homology of 16S rDNA and several molecular techniques already applied to discriminate among them give ambiguous results.The slightly higher variability of the hsp60 gene sequences with respect to the 16S rRNA sequences offers better opportunities to design or develop molecular assays, allowing identification and differentiation of closely related species. hsp60 can be considered an excellent additional marker for inferring the taxonomy of the members of Bifidobacterium genus.ResultsThis work illustrates a simple and cheap molecular tool for the identification of Bifidobacterium species. The hsp60 universal primers were used in a simple PCR procedure for the direct amplification of 590 bp of the hsp60 sequence. The in silico restriction analysis of bifidobacterial hsp60 partial sequences allowed the identification of a single endonuclease (HaeIII) able to provide different PCR-restriction fragment length polymorphism (RFLP) patterns in the Bifidobacterium spp. type strains evaluated. The electrophoretic analyses allowed to confirm the different RFLP patterns.ConclusionsThe developed PCR-RFLP technique resulted in efficient discrimination of the tested species and subspecies and allowed the construction of a dichotomous key in order to differentiate the most widely distributed Bifidobacterium species as well as the subspecies belonging to B. pseudolongum and B. animalis.

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“…Molecular techniques based on polymerase chain reaction (PCR) have been successfully developed and implemented for detection and enumeration of diVerent microorganisms (pathogenic and nonpathogenic) from a wide variety of environments [7,9,21,22]. Molecularbased methodologies have high reproducibility, accuracy, and speciWcity for recognition of minimal diVerences at genomic level for highly related organisms such as those belonging to the Klebsiella (Raoultella) group [10].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of molecular techniques for identification and enumeration of Raoultella terrigena ATCC 33257 in water purifier efficacy testing

Saha

Bechanko

Bestervelt

et al. 2010

J Ind Microbiol Biotechnol

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Raoultella terrigena ATCC 33257, a representative of the coliform group, is commonly used as a challenge organism in water purifier efficacy testing. In addition to being time consuming, traditional culturing techniques and metabolic identification systems (including automated systems) also fail to accurately differentiate this organism from its closely related neighbors belonging to the Enterobacteriaceae group. Molecular-based techniques, such as real-time quantitative polymerase chain reaction (qPCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting, are preferred methods of detection because of their accuracy, reproducibility, specificity, and sensitivity, along with shorter turnaround time. ERIC-PCR performed with the 1R primer set demonstrated stable unique banding patterns (~800, ~300 bp) for R. terrigena ATCC 33257 different from patterns observed for R. planticola and R. ornithinolytica. The primer pair developed from gyraseA (gyrA) sequence of R. terrigena for the SYBR Green qPCR assay using the AlleleID(®) 7.0 primer probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cells and 4.7 fg with genomic DNA. The primer pair was successful in determining the concentration (5.5 ± 0.3 × 10(6) CFU/ml) of R. terrigena from water samples spiked with equal concentration of Escherichia coli and R. terrigena. Based on these results from the ERIC-PCR and the SYBR Green qPCR assay, these molecular techniques can be efficiently used for rapid identification and quantification of R. terrigena during water purifier testing.

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Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium

Cited by 13 publications

References 55 publications

Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria

Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria

Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment

Evaluation of molecular techniques for identification and enumeration of Raoultella terrigena ATCC 33257 in water purifier efficacy testing

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