Whole genome-based safety assessment of Lacticaseibacillus paracasei TISTR 2688, a potential probiotic for oral health care product

Lacticaseibacillus paracasei TISTR 2688, anti-oral pathogen activity possessing probiotic, was originally isolated from fermented termite comb.  In this study, the safety of TISTR 2688 was investigated by whole genome analysis. The whole genome of TISTR 2688 was sequenced with two platforms, Illumina MiSeq and Oxford Nanopore Technologies (ONT). After hybrid assembly and annotation, it was shown that TISTR 2688 contained a singular chromosome of 3,209,739 bp with 46.40% GC content. Four plasmids, 57,771 bp, 65,854 bp, 7,511 bp and 6,877 bp were identified. The strain was confirmed to be Lacticaseibacillus paracasei with the average nucleotide identity (ANI) of 97.78% to the species’ type strain ATCC 25302. TISTR 2688 did not harbor transferable antimicrobial resistance (AMR) genes, genes encoding bile salt hydrolase, and had no pathways for production of critically important antimicrobials for human medicine. Two copies of putative genes encoding D-lactate dehydrogenase were identified in the genome. Moreover, 9 prophage regions including 3 intact prophages, 3 incomplete and 3 questionable prophages were identified. None of the AMR genes were located on any plasmids or prophage regions. This finding together with the results of previous phenotypic assay and acute oral study indicated that L. paracasei TISTR 2688 was proven to be a safe probiotic candidate for human use.