Genomic Analysis for the Safety Assessment of a Potential Probiotic Strain Pediococcus pentosaceus BBS1 Isolated From Lao Fermented Bamboo Shoots (Nor Mai Som)

Abstract

Currently, there is an increasing use of whole-genome sequencing (WGS) studies to investigate the molecular taxonomy, metabolic properties, enzyme capabilities, and bioactive substances of lactic acid bacteria (LAB) species. In this study, the genome of strain Pediococcus pentosaceus BBS1 was sequenced using the Illumina HiSeq. 2500 platform to determine its classification, annotate its main features, and evaluate its safety characteristics. Results showed an average nucleotide identity (ANI) value of 99.60% for Pediococcus pentosaceus BBS1. P. pentosaceus BBS1 genome was composed of a 1,840,613 bp circular chromosome with a GC content of 37.23%, which contained 1778 predicted protein-coding sequences (CDSs). Rapid Annotation using Subsystems Technology (RAST) linked to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that strain BBS1 possesses l-acetate dehydrogenase (l-LDH; EC 1.1.1.27) and d-lactate dehydrogenase (d-LDH; EC 1.1.1.28), which are the genes responsible for lactic acid production. Additionally, it was found to contain linamarase, or β-glucosidases (EC 3.2.1.21), a gene that functions for cyanide degradation. Significantly, the safety studies carried out using WGS confirmed the absence of virulence factors, biogenic amines, and antibiotic-resistance genes in BBS1. Our previous research conducted in this study have shown that BBS1 possesses probiotic features, including tolerance to the simulated artificial gastrointestinal tract, bacterial adhesion, antibacterial activity, and antioxidant function. The findings provided herein significantly enhanced the known information on BBS1, supporting its potential application in promoting health through food products.