16S ribosomal RNA-depletion PCR and its application in cause analysis of yogurt package shrinkage

Fermentative bacteria, the main microbiota in yo-gurt, interfere with the detection of unintended bacte-rial contaminants. The removal of fermentative bacteria and enrichment of unintended bacterial contaminants is a challenging task in bacterial detection. The present study developed a new 16S rRNA-depletion PCR for such enrichment and detection. Specifically, a single -guide RNA was designed and synthesized based on the 16S rRNA sequence of Streptococcus thermophilus, with the highest DNA abundance in the yogurt. The CRISPR-Cas9 system was used to specifically cleave and remove the genomic DNA of the fermentative bacteria, followed by PCR amplification. This method improved the detection sensitivity, simplified the op-eration steps, and reduced the detection cost of PCR analysis. We also used the 16S rRNA-depletion PCR to amplify and detect the unintended bacterial contami-nants in yogurts with shrunken packages and analyzed the underlying reasons to prevent this issue of product quality.

Automated summary

This study developed a new PCR method using the CRISPR-Cas9 system to remove fermentative bacteria in yogurt and enrich unintended bacterial contaminants. The method improved detection sensitivity, simplified operation steps, and reduced detection costs. By analyzing unintended bacterial contaminants in yogurt with shrunken packaging, the underlying reasons for product quality issues were identified.