Development of a High-Throughput Microfluidic qPCR System for the Quantitative Determination of Quality-Relevant Bacteria in Cheese.
Fluidigm
cheese microbiome
cheese quality
fermented food
food microbiology
microbial community composition
microfluidic
real-time qPCR
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2020
2020
Historique:
received:
19
10
2020
accepted:
08
12
2020
entrez:
25
1
2021
pubmed:
26
1
2021
medline:
26
1
2021
Statut:
epublish
Résumé
The composition of the cheese microbiome has an important impact on the sensorial quality and safety of cheese. Therefore, much effort has been made to investigate the microbial community composition of cheese. Quantitative real-time polymerase chain reaction (qPCR) is a well-established method for detecting and quantifying bacteria. High-throughput qPCR (HT-qPCR) using microfluidics brings further advantages by providing fast results and by decreasing the cost per sample. We have developed a HT-qPCR approach for the rapid and cost-efficient quantification of microbial species in cheese by designing qPCR assays targeting 24 species/subspecies commonly found in cheese. Primer pairs were evaluated on the Biomark (Fluidigm) microfluidic HT-qPCR system using DNA from single strains and from artificial mock communities. The qPCR assays worked efficiently under identical PCR conditions, and the validation showed satisfying inclusivity, exclusivity, and amplification efficiencies. Preliminary results obtained from the HT-qPCR analysis of DNA samples of model cheeses made with the addition of adjunct cultures confirmed the potential of the microfluidic HT-qPCR system to screen for selected bacterial species in the cheese microbiome. HT-qPCR data of DNA samples of two downgraded commercial cheeses showed that this approach provides valuable information that can help to identify the microbial origin of quality defects. This newly developed HT-qPCR system is a promising approach that will allow simultaneous monitoring of quality-relevant species in fermented foods with high bacterial diversity, thereby opening up new perspectives for the control and assurance of high product quality.
Identifiants
pubmed: 33488561
doi: 10.3389/fmicb.2020.619166
pmc: PMC7817891
doi:
Types de publication
Journal Article
Langues
eng
Pagination
619166Informations de copyright
Copyright © 2021 Dreier, Berthoud, Shani, Wechsler and Junier.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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