High resolution analysis of multi-strain probiotic products by NGS using innovative molecular markers
Objective
Ensuring the accuracy of microbial composition in probiotic and fermented food products is crucial for quality control. However, standard methods like 16S rRNA-based NGS metabarcoding struggle to differentiate closely related bacterial strains. This limits their effectiveness in industrial settings where precise strain identification is required.
Innovative Solution
A novel approach using HPME markers has been developed to enhance the resolution of microbial identification. These markers are highly variable intergenic sequences flanked by conserved coding regions, making them ideal for targeted PCR amplification and sequencing. Compared to 16S rRNA metabarcoding, the HPME method offers:
- Higher taxonomic resolution, distinguishing between subspecies and strains.
- Accurate species identification, reducing misclassification errors.
- Strain-level discrimination, crucial for assessing product consistency and efficacy.
- Compatibility with existing techniques, such as flow cytometry for microbial quantification.
Practical Implications & Benefits
For practitioners in the probiotics, fermented food, and microbiome industries, this method provides:
- Improved quality control, ensuring product composition aligns with claims.
- Enhanced product stability checks, detecting changes in microbial blends over time.
- Regulatory compliance, by providing detailed microbial composition data.
- Cost-effectiveness, as it minimizes false identifications and batch inconsistencies.
Case Studies
- Bifidobacterium genus: The HPME method successfully identified all five strains in a sample, whereas the standard 16S rRNA approach failed to distinguish between subspecies and introduced false positives.
- Lactiplantibacillus genus: HPME metabarcoding correctly detected all six species in a sample, unlike the 16S rRNA method, which failed to identify L. pentosus and misclassified other sequences.
Additional information
Authors:
A. Del Casale, S. Campana, I. Campedelli, F. Fracchetti
Transparency solutions for transforming the food system
Ongoing | 2022-2026
- Main funding source
- Horizon Europe (EU Research and Innovation Programme)
- Geographical location
- Belgium, Netherlands, Italy, Germany, Greece, Portugal, Spain, France, Finland, Poland, United Kingdom, Norway, Switzerland, Serbia