Development of a Strain-Specific Detection and Quantification Method for <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> HN019 Using WGS-SNP Analysis and qPCR

Development of a Strain-Specific Detection and Quantification Method for <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> HN019 Using WGS-SNP Analysis and qPCR

Accurate quantification of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> HN019, a clinically validated probiotic strain conferring immune modulation, gastrointestinal health, and gut barrier integrity benefits, is essential for diverse applications. To address the crit...

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Bibliographic Details
Main Authors: Da Mao, Lei Zhao, Bo Zhao, Hongbin Xu, Qinghe Zhang
Format: Article
Language:English
Published: MDPI AG 2025-07-01
Series:Microorganisms
Subjects:
<i>Bifidobacterium animalis</i> subsp. <i>lactis</i>
strain-specific
identification
quantification
WGS-SNP
Online Access:https://www.mdpi.com/2076-2607/13/7/1596
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Summary:Accurate quantification of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> HN019, a clinically validated probiotic strain conferring immune modulation, gastrointestinal health, and gut barrier integrity benefits, is essential for diverse applications. To address the critical need for strain-specific detection, we developed a quantitative PCR (qPCR) assay targeting a unique single-nucleotide polymorphism (SNP) within the <i>gal</i>K gene, identified through comparative whole-genome sequencing (WGS) analysis of 31 <i>B. animalis</i> subsp. <i>lactis</i> strains. The assay exhibited exceptional specificity, distinguishing HN019 from 19 other <i>Bifidobacterium</i> strains. Sensitivity tests indicated a detection limit of 0.5 pg of DNA and 10<sup>3</sup> CFU/mL of bacterial cells, making it suitable for industrial-scale applications. Additionally, the method exhibited strong repeatability, reproducibility across different qPCR platforms, and resistance to interference from high cell density of <i>B. animalis</i> subsp. <i>lactis</i> DSMZ 10140. Successful quantification of HN019 in complex multi-strain probiotic powders confirmed its practical reliability. This work establishes a rapid, robust, and scalable tool for precise probiotic strain tracking, addressing critical quality control and regulatory compliance needs within the rapidly expanding probiotic industry.
ISSN:2076-2607

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