Complete genome sequencing and probiotic characterization of promising lactic acid bacterial strains isolated from dairy products in Egyptian markets

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Abstract Background Probiotics refer to live bacteria that, when administered in a sufficiently, exert a beneficial influence on human health. Due to the probiotics' beneficial health advantages, dietary supplements are expanding rapidly as a self-care interest worldwide. It may be beneficial to administer probiotic strains resistant to antibiotics concurrently with an antibiotic treatment. Our study investigates nineteen dairy products collected from Egyptian markets, isolated, identified and underwent a characterization for probiotic features under demanding circumstances as NaCl, acid and bile salt environments. The antibiotic sensitivity test was performed later to the antimicrobial assessment against widespread both negative and positive gram-stained bacteria infecting humans, along with the antiviral evaluation against (SARS-CoV-2), the virus that has disturbed the world recently. Results Out of nineteen investigated isolates, five potential probiotic isolates were examined for probiotic characteristics. Our tested samples were of dairy origin (yogurt, cottage-cheese and sour milk) in Egypt, were identified as Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Pediococcus acidilactici. These promising isolates had withstood stressful factors, such as NaCl, acid, bile salts, and the antimicrobial advance. The genomes were characterized for the physiology, safety, and efficacy of these isolates for probiotic qualities plus the presence of mobile genetic components and prophages that influence the genome's flexibility. They lack virulence factors and pathogenicity, rather than the lack of antibiotic resistance genes. Conclusion Three promising isolates underwent complete genome sequencing with high-throughput second generation technology followed by comprehensive bioinformatic analysis. The results showed that our isolates possess traits enabling resilience to antimicrobial effects and stress factors that might cause problems in the human gut. Several trustworthy genomic analysis methods were used to confirm and provide detailed illustrations of all traits. Genomic analyses confirmed the presence of stable genomes due to including mobile genetic components such as phages and CRISPR clusters, which validate their quality and safe usage for human health.