Genome data of Propionibacterium freudenreichii J117, a functional strain from raw-milk cheese

TL;DR

This paper provides the complete genome sequence of Propionibacterium freudenreichii J117, a food-grade bacterium used in cheese fermentation, to support its safe use in enhancing vitamin B12 in plant-based foods.

Contribution

The novel contribution is the complete genome sequencing and annotation of P. freudenreichii J117, including safety assessment for food applications.

Findings

The genome includes two circular replicons with full annotation of genes, RNAs, and CRISPR arrays.

No plasmid-encoded antibiotic resistance genes were detected, confirming the strain's safety for food use.

Abstract

This dataset reports the complete genome sequence of Propionibacterium freudenreichii strain J117, a food-grade bacterium isolated from Austrian Vorarlberger Bergkäs cheese. The strain was selected for its application in a co-fermentation platform aimed at enhancing vitamin B12 content in plant-based fermented foods. Genomic DNA was extracted from anaerobic cultures grown in yeast extract lactate (YEL) broth and sequenced using PacBio Sequel II long-read technology with SMRT Cell 8 M. High-fidelity (HiFi) reads were generated, and circular consensus sequences (CCS) were assembled using the Improved Phased Assembler (IPA v2).

Genome annotation was performed with Bakta v1.10.4. Antibiotic resistance screening was carried out using the Resistance Gene Identifier (RGI v6.0.3) from the Comprehensive Antibiotic Resistance Database (CARD) via the PROKSEE platform. No plasmid-encoded resistance determinants were identified. The genome comprises two circular replicons and includes full annotation of coding sequences, RNAs, CRISPR array, and pseudogenes.

The raw sequencing data, genome assembly files, and annotation outputs are included in the associated data repository, organized in subfolders for raw reads, assemblies, and analysis results. This dataset supports the related research article: Zhang, R., Chen, L., Zhang, D., Sihvola, J., Chamlagain, B., Olin, M., Piironen, V., & Varmanen, P. Innovative co-fermentation of Propionibacterium freudenreichii and Rhizopus oryzae enhances vitamin B12, riboflavin, and flavor profile components in sweet fermented glutinous rice. Food Chemistry, 503 (2026).

The availability of this genome provides a reference for comparative genomic analysis, functional pathway prediction, and strain development. It also facilitates safety assessment of food-related strains, such as the absence of mobile antibiotic resistance genes, thereby supporting the transparent use of J117 in fermented food applications.