Whole Genome Sequencing and Multi-Omics Analysis of Native Enterococcus faecium for Enhanced Stress Tolerance

In this comprehensive study, the complete genome of a native Enterococcus faecium strain isolated from traditional dairy matrices was sequenced with a high-fidelity coverage of ۱۵۰x, achieving ۹۹.۹% assembly accuracy. Genome annotation identified ۲,۸۵۷ protein-coding genes, ۸۵ regulatory RNAs, and mapped over ۱۲۰ critical metabolic pathways, including those implicated in stress adaptation and antimicrobial biosynthesis. Integrative multi-omics analyses-combining metagenomics (>۱۲,۰۰۰ microbial sequence variants detected), transcriptomics (RNA-seq with an average depth of ۵۰ million paired-end reads), and metabolomics (LC-MS profiling identifying >۶۵۰ unique metabolites) were employed to dissect the molecular responses of E. faecium to industrially relevant stressors such as thermal pasteurization (۷۲°C for ۱۵ seconds) and high-pressure processing (۶۰۰ MPa for ۵ minutes). Differential gene expression analyses revealed significant (p < ۰.۰۰۱) upregulation-up to ۴.۵-fold of two-component signal transduction systems, ABC transporter families, and stress-responsive chaperones under these conditions. Metabolomic profiling demonstrated a ۳.۸-fold elevation in class IIa bacteriocins alongside a ۲.۷-fold increase in bioactive exopolysaccharides, correlating with enhanced antimicrobial efficacy and environmental resilience. Precision genome editing via CRISPR-Cas ۱۲a successfully excised repressors of probiotic functionality, resulting in a ۳۷% increase in acid tolerance (pH ۳.۰) and accelerated proliferation kinetics under processing stress. Advanced bioinformatic modeling leveraging machine learning algorithms integrated multi-omics datasets to achieve a ۹۲% predictive accuracy for microbial population dynamics and metabolic flux under industrial fermentation scenarios. This modeling facilitated a ۱۷% reduction in product loss and a ۲۲% enhancement in pathogen inhibition metrics. The study underscores the potential for engineering highly tailored probiotic starters exhibiting optimized physiological attributes, contributing to prolonged shelf life, improved safety, and sensory quality of fermented dairy products. Furthermore, isolated polysaccharides with antioxidative and antimicrobial properties hold promise for incorporation into intelligent food packaging systems. Collectively, this investigation represents a significant advancement in the functional genomics and synthetic biology of food-grade Enterococcus faecium strains, providing a robust framework for deploying multi-omics-driven strain engineering approaches to elevate industrial food microbiology applications.

کلیدواژه ها:

Precision genome editing ، multi-omics integration ، CRISPR-Cas ۱۲a ، two-component systems ، exopolysaccharide biosynthesis ، metabolic flux modeling