Hybrid genome assembly and comprehensive genomic analysis of Lactiplantibacillus pentosus LP309 reveal its probiotic and technological potential

TL;DR

This study analyzes the genome of Lactiplantibacillus pentosus LP309, revealing its potential as a probiotic and useful in food and biotech.

Contribution

A novel hybrid genome assembly and detailed genomic analysis of Lactiplantibacillus pentosus LP309, highlighting its probiotic and technological applications.

Findings

The LP309 genome includes a circular chromosome and eight plasmids with 3,448 coding sequences.

Over 150 genes related to probiotic traits and technological functions were identified.

Safety assessment confirmed no virulence or antibiotic resistance genes.

Abstract

This study provides an in-depth genomic and functional characterization of Lactiplantibacillus pentosus LP309, a strain isolated from table olive fermentations. The microorganism was sequenced using three next‑generation sequencing platforms—Illumina, PacBio, and Oxford Nanopore Technologies (ONT)—and multiple assembly and polishing strategies were evaluated. Assembly performance and annotation quality metrics were compared across approaches, and the most complete hybrid assembly for this study (Illumina + ONT) was selected for comprehensive genomic characterization.

The complete chromosome was circularized at 3,523,074 bp, and together with eight plasmids, the total genome length reached 3,743,370 bp, comprising 3,448 coding sequences (CDSs) and reflecting the genomic complexity of LP309 strain. Taxonomic assignment based on Average Nucleotide Identity confirmed the species identity, while functional annotation predicted the presence of two bacteriocin and two exopolysaccharide biosynthesis clusters. Additionally, over 150 genes related to the probiotic and technological potential of the strain were also identified, including those involved in adhesion, acid stress resistance, vitamin biosynthesis, and carbohydrate metabolism, among others. Safety assessment confirmed the absence of genes associated with virulence, antibiotic or acquired antimicrobial resistance. Mobilome analysis revealed four prophages, 133 insertion sequences, and four genomic islands, while no integrons were detected.

This in silico study has revealed the strong technological relevance and probiotic potential of LP309, establishing this plant-based bacterium as a safe and functionally versatile candidate for applications in the food and biotechnology industries.

The online version contains supplementary material available at 10.1186/s12864-026-12678-y.

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