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Identification and Classification for the Lactobacillus casei Group.

Chien-Hsun Huang1, Shiao-Wen Li2, Lina Huang1

  • 1Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.

Frontiers in Microbiology
|September 7, 2018
PubMed
Summary

Accurate identification of the Lactobacillus casei group, including Lactobacillus paracasei and Lactobacillus rhamnosus, is now possible using novel methods. These techniques improve upon traditional gene sequencing and DNA hybridization for bacterial classification.

Keywords:
Lactobacillus casei groupMALDI-TOF MSMLSAspecies-specific PCRwhole genome sequence

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Area of Science:

  • Microbiology
  • Bacterial Taxonomy
  • Probiotics Research

Background:

  • The Lactobacillus casei group, comprising L. casei, L. paracasei, and L. rhamnosus, is taxonomically complex.
  • Traditional 16S rRNA gene sequencing and DNA-DNA hybridization methods present challenges for accurate species identification within this group.
  • Accurate classification is crucial due to the commercial value of these bacteria as probiotics.

Purpose of the Study:

  • To develop rapid and accurate methods for identifying L. casei group strains at species and subspecies levels.
  • To establish reliable identification techniques that overcome limitations of current genotypic and phenotypic methods.
  • To refine the taxonomic classification of the L. casei group, including the potential description of new species.

Main Methods:

  • Phylogenetic analysis using concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, yycH).
  • Development of a multiplex minisequencing assay based on SNP-specific primers (dnaK) and species-specific primers (mutL).
  • Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis with a custom database.

Main Results:

  • Phylogenetic analysis delineated four species clusters: L. casei, L. paracasei, L. rhamnosus, and Lactobacillus chiayiensis sp. nov.
  • The multiplex minisequencing assay accurately identified strains at the species level.
  • MALDI-TOF MS successfully differentiated species and subspecies within the L. casei group, with distinct subspecies-specific peaks for L. paracasei.

Conclusions:

  • Novel methods based on housekeeping gene sequences and MALDI-TOF MS provide rapid and accurate identification of L. casei group strains.
  • These methods facilitate precise taxonomic classification, including the identification of L. chiayiensis sp. nov. and 'Lactobacillus zeae'.
  • The developed techniques offer practical solutions for routine laboratory identification and classification of these commercially important bacteria.