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

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 16 S 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 16 S rRNA sequence-based identification and represented genome-based speciation.

Automated summary

Analysis of untranscribed DNA sequences in intergenic spacer regions (ISR) in groESL resolved ambiguity between closely related GRAS and non-GRAS species. Using groESL-ISR-specific primers for PCR sequencing accurately differentiated L. plantarum and L. pentosus, showing more accuracy than 16S rRNA sequences. Major probiotics species were grouped based on ISR sequences, which correlated with core-genome differentiation, indicating ISR-based species identification provides more accurate results than 16S rRNA-based identification and represents genome-based speciation.