Molecular typing tools for identifying and characterizing lactic acid bacteria: a review

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.

Probiotic lactobacilli in formulas and hygiene products for the health of the urogenital tract

“…These molecular techniques include Sanger sequencing of 16S rRNA of bacterial colonies, terminal restriction fragment length polymorphism of 16S rRNA, qPCR, and next-generation sequencing that have modified the concept of the microbiome versatilities and more specifically Lactobacillus identification. [2][3][4][5][6][7][8][9][10][11][12][13] Then, the majority of the indigenous microbiota exists in a mutually beneficial relationship with the host, while few are opportunistic pathogens. 14 An important body site providing a habitat for the development of structured microbial communities is the vaginal tract, which is broadly colonized by microorganisms known as the vaginal microbiota (VM).…”

“…In such a way that the HM is a complex system of many microbial communities, deeply described in terms of composition, diversity, and dynamics, known thanks to the use and update of massively parallel sequencing and other high throughput approaches available, indicating the long list of eukaryotes, archaea, bacteria, and viruses detected. These molecular techniques include Sanger sequencing of 16S rRNA of bacterial colonies, terminal restriction fragment length polymorphism of 16S rRNA, qPCR, and next‐generation sequencing that have modified the concept of the microbiome versatilities and more specifically Lactobacillus identification 2–13 …”

Potential Probiotic Pediococcus pentosaceus M41 Modulates Its Proteome Differentially for Tolerances Against Heat, Cold, Acid, and Bile Stresses

“…The extensive applications of LAB in the food industry make it imperative to link their important characteristics with their corresponding genes and proteins ( Sharma et al, 2020 ). Stress responsive genes and proteins could be helpful in marker-assisted selection of LAB which are more resistant to adverse environments.…”

Multilocus Sequence Typing of Leuconostoc mesenteroides Strains From the Qinghai-Tibet Plateau

“…Therefore, genotypic methods were playing important roles in phylogenetic classification and identification of bacterial species. Till now, many molecular methods had been used for the typing of Leuconostoc genus like pulsed-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD)-PCR, repetitive element palindromic PCR (rep-PCR), and multilocus sequence typing (MLST) ( Vihavainen and Bjorkroth, 2009 ; Alegria et al, 2013 ; Sharma et al, 2018 , 2020 ). MLST was a technique for distinguishing accurately between different isolates within a species.…”