Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

Abstract

Taxonomic relationships between <i>Lactobacillus casei</i>, <i>Lactobacillus paracasei</i> and <i>Lactobacillus zeae</i> have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains <i>L. casei</i> ATCC 393^T and <i>L. zeae</i> ATCC 15820^T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that <i>L. casei</i> could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (<i>dnaJ</i>, <i>dnaK</i>, <i>mutL</i>, <i>pheS</i> and <i>yycH</i>) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the <i>L. zeae</i> strains, and supported an emended the description of the name of <i>Lactobacillus zeae</i> (ex Kuznetsov 1956) Dicks <i>et al</i>. 1996, with ATCC 15820^T (=DSM 20178^T=BCRC 17942^T) as the type strain.