Bioinformatics analysis of the genome of E. faecalis E-10 strain isolated from cow endometrium

Studying the microbiome of the cow’s reproductive system is crucial for maintaining the animals’ reproductive capacity. In 2025, the E. faecalis E-10 strain was isolated from the endometrium of a healthy Ayrshire cow kept at the Valaam Monastery eco-farm. The aim of the study was a whole-genome analysis of the strain using the MiSeq sequencer (Illumina, Inc., USA) and bioinformatics tools, including the Trimmomatic-0.38 (http://www.usadellab.org/cms/?page=trimmomatic), SPAdes-3.11.1 (https://github.com/ablab/spades), QUAST Version: 5.0.2 (http://quast.sf.net), BV-BRC (https://www.bv-brc.org), RAST (https://rast.nmpdr.org), KEGG (https://www.kegg.jp), Prokka (https://github.com/tseemann/prokka), and HMMER (hmmsearch) (https://hmmer.org) databases. Whole genome analysis of the E. faecalis E-10 strain showed that the genome consists of 108 contigs and has a total length of 2,882,409 bp, with a GC content of 37.49%. Analysis of the antimicrobial activity of the strain showed that the largest growth inhibition zones (up to 29 ± 1.5 mm) were noted for test cultures of Clostridium perfringens, Streptococcus agalactiae, Aspergillus spp. and Penicillium spp. The genes for the synthesis of organic acids were found in the genome of E. faecalis E-10, such as ldh1 and ldh2 (associated with the synthesis of L- and D-lactic acids), pta1/2 and ackA (responsible for acetic acid), pflA/B (for formate), and fumC, frdA, and mae (for succinate). Genes for resistance to oxidative and osmotic stress were also identified. These included genes encoding glutathione biosynthesis, the CoA-disulfide thiol disulfide redox system, the choline and betaine uptake system, and betaine biosynthesis. Adhesion proteins, such as Sortase A, the WxL repertoire (more than 10 proteins), and LysM multidomain proteins (including autolysins), were also detected. These results indicate a potential role for E. faecalis E-10 in maintaining a favorable microbial balance in the endometrium.