A new method for quantitative detection of Lactobacillus casei based on casx gene and its application

BMC Biotechnol. 2019 Dec 10;19(1):87. doi: 10.1186/s12896-019-0587-6.


Background: The traditional method of bacterial identification based on 16S rRNA is a widely used and very effective detection method, but this method still has some deficiencies, especially in the identification of closely related strains. A high homology with little differences is mostly observed in the 16S sequence of closely related bacteria, which results in difficulty to distinguish them by 16S rRNA-based detection method. In order to develop a rapid and accurate method of bacterial identification, we studied the possibility of identifying bacteria with other characteristic fragments without the use of 16S rRNA as detection targets.

Results: We analyzed the potential of using cas (CRISPR-associated proteins) gene as a target for bacteria detection. We found that certain fragment located in the casx gene was species-specific and could be used as a specific target gene. Based on these fragments, we established a TaqMan MGB Real-time PCR method for detecting bacteria. We found that the method used in this study had the advantages of high sensitivity and good specificity.

Conclusions: The casx gene-based method of bacterial identification could be used as a supplement to the conventional 16 s rRNA-based detection method. This method has an advantage over the 16 s rRNA-based detection method in distinguishing the genetic relationship between closely-related bacteria, such as subgroup bacteria, and can be used as a supplement to the 16 s rRNA-based detection method.

Keywords: 16 s rRNA; Cas; Lactobacillus casei; Rapid detection method; TaqMan MGB RT-PCR.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Typing Techniques / methods*
  • Base Sequence
  • CRISPR-Associated Proteins / genetics*
  • Lactobacillus casei / classification
  • Lactobacillus casei / genetics
  • Lactobacillus casei / isolation & purification*
  • Phylogeny
  • Polymerase Chain Reaction


  • Bacterial Proteins
  • CRISPR-Associated Proteins