Rapid identification of Bacteroides dorei using novel specific target revealed by pan-genome analysis and its application in food

Abstract

Bacteroides dorei is a promising candidate for the next generation probiotics (NGP), but its accurate identification remains challenging due to its close taxonomic relationship with other Bacteroides species. This study aimed to mine the novel specific molecular target for detecting Bacteroides dorei. Using pan-genome analysis and PCR validation, species-specific target genes with a size of 193 bp were identified, and the specificity of the designed primer pair (30 bp) for this molecular target was confirmed. The PCR assay demonstrated high applicability for detecting target and/or nontarget strains in three simulated food systems, yielding no false-positive or false-negative results. Additionally, a qPCR method was developed for quantifying Bacteroides dorei, with a linear detection range from 1×108 to 1×101 CFU/mL and an R2 value greater than 0.98. This method exhibited accurate and sensitive detection capabilities suitable for both food and feces samples. Overall, our study established PCR and qPCR assays for the rapid identification of Bacteroides dorei, advancing the exploration of Bacteroides species and the application of detection for NGPs in functional foods across various product forms.