The groESL ISR sequence-based species-specific identification of GRAS and non-GRAS Lactiplantibacillus as an alternative to 16S rRNA sequencing

Abstract The untranscribed DNA sequences of the intergenic spacer regions (ISR) in the groESL were analyzed to resolve the ambiguity within phylogenetically close GRAS and non-GRAS species. The sequencing results of amplified polymerase chain reaction (PCR) products using groESL-ISR-specific primers accurately distinguished L. plantarum and L. pentosus, which were not distinguished by 16S rRNA sequences. Furthermore, the 20 selected major probiotics species were divided into several groups according to the length (22–91 bp) and homology (65-99%) of their ISR sequences, and this discrimination was consistent with core-genome-based differentiation. Therefore, ISR sequence-based species identification showed more accurate results than 16S rRNA sequence-based identification and represented genome-based speciation.