Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
Highlights
Nine whole genomes belonging to L. argentoratensis, L. garii, L. herbarum, L. modestisalitolerans, L. nangangensis, L. paraplantarum, L. pentosus, L. plajomi, and L. xiangfangensis were annotated using Prokka [37] to identify the coding sequences
Researchers have employed comparative sequences of the housekeeping genes dnaJ, dnaK, hsp60, phenylalanyl t-RNA synthase alpha subunit (pheS), recA, RNA polymerase alpha subunit (rpoA), rpoB, and tuf to distinguish the members of the L. plantarum group [11,45,51,53,54]
Researchers have established species-specific polymerase chain reaction (PCR) primers that are targeted to the variable regions of the recA gene for species identification of L. argentoratensis, L. paraplantarum, L. pentosus, and L. plantarum [9,48]
Summary
Following reclassification of Lactobacillus according to physiological criteria, cladespecific signature genes, core genome phylogeny, organism ecology, and pairwise average amino acid identity, this varied genus comprises of 25 genera, with 23 of them being novel [1]. This change to the taxonomy has affected major probiotic Lactobacillus species; for example, Lactobacillus plantarum has become Lactiplantibacillus plantarum. Because the new genera suggested for this group all still begin with an “L”, the abbreviated genus and species names are unchanged. L. plantarum is a versatile lactic acid bacteria (LAB)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
