Deciphering probiotic potential: a comprehensive guide to probiogenomic analyses

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Probiotics show promise for gut health, immunity, and digestion, with growing interest in food and pharmaceutical applications.
• Traditional in vitro probiotic identification methods face limitations in reproducibility, strain discovery, safety assessment, and understanding mechanisms.
• Genomic analysis offers a cost-effective way to explore probiotic strains and their beneficial effects.

Purpose of the Study:

• To establish a gold-standard probiogenomic analysis pipeline for screening probiotic potential using whole-genome sequencing.
• To develop a comprehensive workflow for identifying safety features, genomic plasticity, and probiotic markers.
• To create an extensive database of genes associated with probiotic functions.

Main Methods:

• Whole-genome sequencing of probiotic strains.
• Development of a comprehensive bioinformatics workflow for probiogenomic analysis.
• Screening for safety-related genes, genomic plasticity, and known probiotic markers.
• Compilation of a database of 243 genes potentially linked to probiotic functions.

Main Results:

• A standardized probiogenomic analysis pipeline was established.
• The workflow enables comprehensive screening of probiotic potential directly from genome sequences.
• A database of 243 genes associated with probiotic functions was compiled.

Conclusions:

• Probiogenomic analysis via whole-genome sequencing provides a robust and efficient method for probiotic strain evaluation.
• The developed pipeline and database offer a gold-standard approach for advancing probiotic research and application.
• This method enhances the understanding of molecular mechanisms underlying probiotic health benefits.