Genome-Based in silico Evaluation of the Biosafety and Probiotic Traits of Limosilactobacillus fermentum J23 Isolated from Artisanal Mexican Cheese

ABSTRACT

Comprehensive in silico analysis aimed to identify the genes involved in the biosafety and probiotic features of Limosilactobacillus fermentum J23 was performed. The strain had a single circular chromosome of 2,004,882 base pairs (bp), with a Guanine + Cytosine (G + C) content of 51.74%. The chromosome contained 2,001 genes predicted as protein-coding sequences (CDS), 86 pseudogenes, 56 tRNAs, five rRNAs, and three ncRNAs. The in silico analysis demonstrated the absence of risk-related genes corresponding to transferable/acquirable antibiotic resistance, virulence factors, toxic metabolites, and detrimental metabolic/enzymatic activities. The strain was predicted as nonpathogenic to humans and the presence of a variety of genes potentially related to its probiotic profile were revealed, including those of carbohydrate metabolism and transport, adhesion and aggregation ability, stress/adaptive response, CRISPR/Cas adaptive immunity, and immunomodulation. These findings highlight the probiotic potential of L. fermentum J23 and provide genomic clues of its biosafety to advance its future applications.

KEYWORDS:

• Limosilactobacillus fermentum
• artisanal cheese
• draft genome sequence
• biosafety
• probiotic profile

Acknowledgments

We gratefully acknowledge the National Council of Humanities, Science, and Technology (CONAHCyT) of Mexico for the postgraduate scholarship granted to author Cecilia Castro-López. We also thank the National Network on Research, Innovation, and Technological Development on Functional Foods and Nutraceuticals-ALFANUTRA, CONACyT‐244208 and to the Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo (CYTED), Red para el fomento de la Calidad e Inocuidad en Queserías Artesanales en Iberoamérica-QuesArte Iberoamérica (P122RT0126).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Genome sequence and assembly of L. fermentum J23 were deposited in the NCBI-GenBank under accession number JAMDNV000000000. Data associated with this study are available from the corresponding author upon reasonable request.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/08905436.2024.2305959.

Additional information

Funding

This study was funded through CONAHCyT research project [CB2017-2018, A1-S-53161].