Rapid species- and subspecies-specific level classification and identification of Lactobacillus casei group members using MALDI Biotyper combined with ClinProTools

Publication date: Available online 15 November 2017
Source:Journal of Dairy Science
Author(s): Chien-Hsun Huang, Lina Huang
Using common taxonomic methods such as 16S rDNA sequencing and physiological and biochemical analysis to identify members of the Lactobacillus casei group (LCG) is time-consuming, expensive and inaccurate. In this study, we applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to rapid discriminate LCG strains by creating an analytical in-house database (IHDB) and to develop a classification model for subspecies-level differentiation based on MS biomarkers using ClinProTools bioinformatics software (Bruker Daltonics, Billerica, MA). Genotypic methods (housekeeping gene sequencing and species-specific PCR) were also established to validate the MALDI-TOF MS platform. A total of 48 LCG reference strains were correctly identified at the species level (mean score: 2.45 ± 0.1) by using MALDI-TOF MS with an IHDB and had high score values, which was in accordance with results from mutL gene sequencing and specific PCR-based methods. However, one strain that was identified as L. casei had a relatively low score value (2.02 ± 0.02), lower sequence similarities (mutL: 90.4%), and failed to amplify a species-specific amplicon; it may therefore represent an undescribed novel species. In addition, after implementation of the classification model (based on 2 biomarker peaks: m/z 4,930 and 5,303), L. paracasei strains could be clearly and easily differentiated to the subspecies level. Afterward, 7 LCG-related isolates from different probiotic samples were analyzed and accurately identified. Our data demonstrate the high-resolution performance of MALDI-TOF MS for fast and accurate demarcation of LCG strains when used with an IHDB coupled to ClinProTools; this methodology can serve as an alternative for quality control of probiotic products.



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