Research Details

This part contains the following information:
a. Executive summary
The growing demand for functional foods and probiotic-based pharmaceutical products has intensified the need for efficient, reliable, and cost-effective methods for evaluating probiotic safety and functionality. Traditional probiotic characterization methods rely heavily on labor-intensive phenotypic and biochemical assays, which may not adequately distinguish closely related strains or comprehensively assess safety-related genetic determinants. Advances in whole genome sequencing (WGS) now provide a powerful in silico alternative for rapid strain-level identification and preliminary probiotic evaluation.
This study investigated the probiotic potential of a bacterial isolate obtained from the indigenous food crop Dioscorea esculenta collected in Ilocos Norte, Philippines. Lesser yam is recognized for its rich phytochemical and prebiotic composition, making it a promising ecological niche for beneficial lactic acid bacteria. The isolate, designated strain SCA72564, underwent whole genome sequencing followed by de novo genome assembly and comprehensive bioinformatics analyses.
Genome quality assessment demonstrated that the assembled genome was relatively complete and of high quality. Whole genome-based taxonomic analysis identified the isolate as Lacticaseibacillus paracasei subsp. paracasei. Safety evaluation revealed the absence of virulence-associated genes, antimicrobial resistance genes, and pathogenic determinants, indicating that the strain is genetically safe for further probiotic consideration.
Functional genome annotation identified several genes associated with desirable probiotic properties. These include genes involved in stress tolerance, immunomodulation, adhesion capability, and antimicrobial compound production, all of which contribute to probiotic survival and beneficial interaction within the gastrointestinal environment. Additionally, the genome exhibited a substantial number of genes related to carbohydrate metabolism, suggesting strong metabolic adaptability and the capacity to utilize a broad range of complex dietary carbohydrates.
The study also detected biosynthetic gene clusters linked to the production of secondary metabolites with potential pharmaceutical and biotechnological applications. These findings highlight the usefulness of WGS as a rapid and cost-effective approach for the initial screening and characterization of probiotic candidates prior to extensive laboratory validation.
Overall, the study demonstrates that strain SCA72564 possesses promising probiotic and functional characteristics while meeting important genomic safety criteria. Furthermore, the discovery of this beneficial microorganism from an indigenous crop emphasizes the untapped potential of Philippine food plants such as lesser yam as valuable sources of novel probiotic strains. The research contributes to the growing body of evidence supporting the integration of genomics and bioinformatics in probiotic development and underscores opportunities for value addition to indigenous agricultural resources through functional food and pharmaceutical innovation.

The findings demonstrate that strain SCA72564 possesses promising probiotic characteristics and satisfies important genomic safety criteria, supporting its potential use in functional food and pharmaceutical development. The study also highlights the effectiveness of WGS-based analyses for the preliminary evaluation of probiotic candidates and emphasizes the value of indigenous crops such as Dioscorea esculenta as potential sources of beneficial microorganisms. This research contributes to the growing application of genomics and bioinformatics in probiotic discovery and supports the development of value-added products from native agricultural resources.