Probiotic Strain Identification: Current and Future Approaches
DOI:
https://doi.org/10.5530/ajphs.2026.16.88Keywords:
Probiotic strain identification, Strain identification approaches, ProbioticsAbstract
Health benefits of Probiotic are highly strain-specific, making accurate strain identification essential for safety, efficacy, correct labeling, and regulatory compliance. Over time, identification approaches have evolved from traditional culture-based and biochemical methods to advanced molecular and genomic techniques. Current methods include phenotypic and biochemical analyses, strain typing (PFGE, RAPD, MLST), mass-based fingerprinting (MALDI-TOF MS), targeted molecular assays (strain-specific PCR, qPCR, digital PCR), and high-resolution genomic tools such as 16S rRNA gene sequencing, whole-genome sequencing (WGS), and metagenomics. These techniques vary in resolution, turnaround time, cost, and suitability for clinical trials or industrial applications. Despite significant progress, challenges remain in distinguishing closely related strains, detecting low-abundance strains in complex samples, database standardization, nomenclature, and regulatory harmonization. Emerging approaches such as pangenome analysis, long-read sequencing, functional marker discovery, mobile genomic platforms, and AI-driven genomic analysis are expected to overcome current limitations and shape the future of probiotic strain identification. This review mentions the kind of extensive analysis of the present and emerging techniques of identifying the bacterial strain of probiotics, along with the technological constraints and innovative developments in the coming years in the sector.
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