Genomic Sequence of Streptococcus salivarius MDI13 and Latilactobacillus sakei MEI5: Two Promising Probiotic Strains Isolated from European Hakes (Merluccius merluccius, L.)

Abstract

Simple Summary: In fish farming, diseases have commonly been fought with the abusive use of antibiotics, which have caused antibiotic (multi)resistances in bacteria. Consequently, it is necessary to explore safe and environmentally friendly alternative approaches to improve the fish health and avoid the treatment of bacterial diseases with antibiotics such as the use of probiotics. This study focuses on bioinformatic and functional analyses of the genome sequences of Streptococcus salivarius MDI13 and Latilactobacillus sakei MEI5, two Lactic Acid Bacteria (LAB) isolated from the gut of European hakes (Merluccius merluccius, L.), a highly valued marine fish for Spanish gastronomy. The potential probiotic characteristics of both bacteria, and the lack of antibiotic resistance genes and virulence were confirmed. In addition, genes encoding three antimicrobial peptides (known as bacteriocins) were identified in the genome of S. salivarius MDI13. One of these in vitro-synthesized bacteriocins (BlpK) showed antimicrobial activity against two fish pathogens (namely Lactococcus garvieae and Streptococcus parauberis). Altogether, our results suggest that S. salivarius MDI13 and L. sakei MEI5 have a strong potential as probiotics to prevent bacterial diseases in fish farming.

Abstract: Frequently, diseases in aquaculture have been fought indiscriminately with the use of antibiotics, which has led to the development and dissemination of (multiple) antibiotic resistances in bacteria. Consequently, it is necessary to look for alternative and complementary approaches to chemotheraphy that are safe for humans, animals, and the environment, such as the use of probiotics in fish farming. The objective of this work was the Whole-Genome Sequencing (WGS) and bioinformatic and functional analyses of S. salivarius MDI13 and L. sakei MEI5, two LAB strains isolated from the gut of commercial European hakes (M. merluccius, L.) caught in the Northeast Atlantic Ocean. The WGS and bioinformatic and functional analyses confirmed the lack of transferable antibiotic resistance genes, the lack of virulence and pathogenicity issues, and their potentially probiotic characteristics. Specifically, genes involved in adhesion and aggregation, vitamin biosynthesis, and amino acid metabolism were detected in both strains. In addition, genes related to lactic acid production, active metabolism, and/or adaptation to stress and adverse conditions in the host gastrointestinal tract were detected in L. sakei MEI5. Moreover, a gene cluster encoding three bacteriocins (SlvV, BlpK, and BlpE) was identified in the genome of S. salivarius MDI13. The in vitro-synthesized bacteriocin BlpK showed antimicrobial activity against the ichthyopathogens Lc. garvieae and S. parauberis. Altogether, our results suggest that S. salivarius MDI13 and L. sakei MEI5 have a strong potential as probiotics to prevent fish diseases in aquaculture as an appropriate alternative/complementary strategy to the use of antibiotics.