Deciphering the Genomic Traits of Multi-Enterocin-Producing E. faecium 1702 from Bottarga: A WGS-Based Characterization

TL;DR

This study uses whole-genome sequencing to analyze a probiotic E. faecium strain with multiple bacteriocin and anticancer-related genes, suitable for biotech and health applications.

Contribution

The study identifies a novel E. faecium strain with multiple probiotic and biotechnological traits through whole-genome sequencing.

Findings

The E. faecium 1702 strain has a genome size of 2,621,416 bp and belongs to the sequence type ST722.

The strain produces three enterocins and harbors genes for anticancer and GABA-related activities.

No clinically relevant antibiotic resistance or virulence factor genes were detected in the strain.

Abstract

Enterococcus spp. produce diverse bioactive molecules used for biotechnological purposes or as probiotic agents for livestock and human health. The main aim of this study was to decipher the genetic traits using whole-genome sequencing (WGS) of a bacteriocinogenic Enterococus faecium 1702 strain showing diverse probiotic traits. Genetic traits of the strain were determined by performing WGS using the NovaSeq6000 platform followed by consecutive sequence analysis using appropriate software. WGS showed that the genome of the E. faecium 1702 strain has a size of 2,621,416 bp, with a GC content of 38.03%. The strain belonged to the sequence type ST722 not known as a human clonal lineage. The strain was free of genes encoding clinically relevant antibiotic resistance; in addition, genes encoding sensu stricto virulence factors, plasmids, and prophages were not detected. Annotations through the Prokaryotic Genomes Automatic Annotation Pipeline (PGAP) tool revealed 2413 coding sequencing entries (CDC) out of 2521 predicted chromosomal genes. The functional annotation of the whole genome through the KEGG database using KofaScan revealed several genes related to several biological activities, including metabolic process, carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism. The strain harbored three entero-bacteriocins (enterocins) encoded by entA, entB, and entX (enterocin X-alpha and X-beta) genes. Interestingly, the strain harbored the ansB, glsA, and arcA genes encoding L-asparaginase, L-glutaminase, and arginine deiminase, respectively, known for their anticancer activities. E. faecium 1702 harbored the gadB, gadC, and gadR genes implicated in gamma(γ)-aminobutyric acid (GABA) production, which is known for its analgesic, anti-anxiety, hypotensive, diuretic, and antidiabetic effects. The WGS findings and phenotypic traits of E. faecium 1702 revealed significant features that allow for its use as a probiotic or for biotechnological and pharmaceutical applications.

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