The composition of probiotic species and the number of viable cells are essential to the quality of composite probiotics products. Two commercial composite probiotic solid beverages and five probiotic species (six strains) contained in the products were studied in this research. The metagenomic sequencing and the average nucleotide identity (ANI) analysis were conducted to accurately identify probiotic composition at the species level. Through selection of species-specific PCR primers and optimization of key parameters of propidium monoazide-quantitative PCR (PMA-qPCR) method, the number of viable probiotic cells of each species were quantitatively detected. The results showed that four bins obtained from the metagenomic data of product 1 were identified as Bifidobacterium animalis subsp. lactis, Lactobacillus rhamnosus, Lactobacillus fermentum, and Bifidobacterium breve, and the number of viable cells detected by PMA-qPCR were 4.86×109, 4.33×109, 3.95×108 and 6.38×106 CFU/g respectively. Four bins obtained from metagenomic data of product 2 were identified as L. rhamnosus, L. plantarum, L. fermentum, and B. animalis subsp. lactis, and the number of viable cells were 3.12×109, 1.53×109, 9.36×108 and 4.16×108 CFU/g respectively. There were no significant differences (P>0.05) between the results of total viable counts in two products obtained by PMA-qPCR method and plate counting method. The probiotics identification results at the species level in this study are consistent with the products' claims. Except for Bifidobacterium breve, the detection results of the number of viable cells for other five species were basically consistent with the products addition. The methods applied in this study can accurately identify the species composition, and can quickly, specifically and accurately quantify the number of viable cells of each probiotic species in the products, which could provide technical support for the quality control of composite probiotic products.
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