Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture

Dietary manipulations using probiotics may contribute to the sustainable development of aquaculture. For probiotic applications, their traits, safety profiles, and functional characteristics should be explored. Whole genome sequencing (WGS) can be an informative tool in this regard. We initiated this study to obtain genomic insights into S. solea gut-associated bacteria. Bacteria ( n = 20) exhibiting probiotic characteristics were subjected to DNA extraction. A mixture comprising equimolar concentrations of each bacterial DNA was prepared and analyzed through WGS. BV-BRC, metaSPAdes, MetaBAT2, DAS Tool, and PATRIC were used for taxonomic profiling, metagenome assembly, genome binning, comprehensive genome annotation, and subsystem analysis, respectively. For tree construction, MUSCLE and RaxML were employed. Fourteen bins comprising Actinomycetota , Bacillota , Bacteroidota, and Pseudomonadota were generated. Among these, the bin comprising the genome of Enterococcus faecium was selected. Its genome comprises 129 contigs with 2,944 coding sequences (CDSs). Genes associated with metabolism, protein processing, stress response, defense and virulence, cellular processes, and cell envelope were identified. Pathways identified included fatty acid and ketone body biosynthesis, glycerolipid and glycerophospholipid metabolism, linoleic acid metabolism, and self-defense mechanisms. This study confirmed the probiotic efficiencies of E. faecium . Hence, this bacterium might be employed as a fish feed supplement in aquaculture.