A Comprehensive Approach to Candidate Probiotic Screening through Nanopore Sequencing and Bioinformatic Analysis
Abstract
Objective: This study aimed to screen and evaluate probiotic properties in bacterial strains isolated from fermented foods and animal feces, using nanopore sequencing and bioinformatic analysis.
Material and Methods: Thirty bacterial strains were isolated from local foods and animal feces within Songkhla, Thailand. After excluding seven pathogenic strains, the remaining 23 strains underwent Deoxyribonucleic Acid (DNA) extraction and whole-genome sequencing using the MinION™ platform from Oxford Nanopore Technologies (ONT). The genomes were then assembled and annotated using bioinformatics analysis to evaluate their probiotic traits and safety profiles.
Results: Genome assembly statistics revealed considerable variability in genome sizes and contig lengths among the strains, with the N50 values ranging from 326,094 bp to 3,226,988 bp. None of the 23 selected strains contained virulence genes associated with significant health risks; confirming their safety. Comprehensive genetic analysis identified key probiotic genes related to acid stress resistance, adhesion, antioxidant activity, bile resistance, and synthesis of beneficial substances; underscoring their potential efficacy in promoting host health.
Conclusion: Whole-genome sequencing, using ONT, combined with bioinformatic analysis, is an effective approach for identifying probiotic strains and predicting their functional properties. This method provides a comprehensive understanding of their potential health benefits and ensures their safety for consumption.
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