Molecular typing tools for identifying and characterizing lactic acid bacteria: a review
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Molecular typing tools for identifying and characterizing lactic acid bacteria: a review Anshul Sharma1,2 • Sulhee Lee3 • Young-Seo Park4
Received: 1 May 2020 / Revised: 21 July 2020 / Accepted: 24 July 2020 Ó The Author(s) 2020
Abstract Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.
& Young-Seo Park [email protected] 1
Department of Food and Nutrition, Gachon University, Seongnam 13120, Republic of Korea
2
Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
3
Research Group of Healthcare, Korea Food Research Institute, Wanju 55365, Republic of Korea
4
Department of Food Science and Biotechnology, Gachon University, Seongnam 13120, Republic of Korea
Keywords Lactic acid bacteria Probiotics DNA RNA Fingerprinting Typing Abbreviations AFLP Amplified fragment length polymorphism ARDRA Amplified ribosomal DNA restriction analysis Bif. Bifidobacterium DGGE Denaturing gradient gel electrophoresis ERIC-PCR Enterobacterial repetitive intergenic consensus-PCR ESI Electrospray ionization FLOW-FISH Flow cytometry-fluorescence in situ hybridization Lac. Lactococcus Lb. Lactobacillus Leu. Leuconostoc MALDI-TOF Matrix-assisted laser desorption/ ionization-time of flight MLST Multilocus sequence typing MS Mass spectrometry NGS Next-generation sequencing P. Pediococcus PFGE Pulse field gel electrophoresis RAPD Random amplified polymorphic DNA RFLP Restriction fragment length polymorphism Rep-PCR Repetitive extragenic palindromic PCR S. Saccharomyces SNP Single nucleotide polymorphism St. Streptococcus TGGE Temperature gradient gel electrophoresis WGS Whole-genome sequencing
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Overview There is a growing interest in the identification of industrially relevant and beneficial microbial strains owing to their heterogeneity and ubiquitous nature. Simple morphological characterization of these microorganisms is ineffective in documenting a
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