Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/10/2553 |
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| author | Despoina E. Kiousi Dimitrios M. Karadedos Anastasia Sykoudi Panagiotis Repanas Christina S. Kamarinou Anthoula A. Argyri Alex Galanis |
| author_facet | Despoina E. Kiousi Dimitrios M. Karadedos Anastasia Sykoudi Panagiotis Repanas Christina S. Kamarinou Anthoula A. Argyri Alex Galanis |
| author_sort | Despoina E. Kiousi |
| collection | DOAJ |
| description | Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, <i>Lactiplantibacillus plantarum</i> L125 and <i>Lp. pentosus</i> L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS. |
| first_indexed | 2024-03-10T21:01:30Z |
| format | Article |
| id | doaj.art-4d5d5bdedfb54ecdb55d6ae382187ae6 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:01:30Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-4d5d5bdedfb54ecdb55d6ae382187ae62023-11-19T17:28:31ZengMDPI AGMicroorganisms2076-26072023-10-011110255310.3390/microorganisms11102553Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based PrimersDespoina E. Kiousi0Dimitrios M. Karadedos1Anastasia Sykoudi2Panagiotis Repanas3Christina S. Kamarinou4Anthoula A. Argyri5Alex Galanis6Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceDepartment of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceDepartment of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceDepartment of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceDepartment of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceInstitute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, GreeceDepartment of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, GreeceProbiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, <i>Lactiplantibacillus plantarum</i> L125 and <i>Lp. pentosus</i> L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.https://www.mdpi.com/2076-2607/11/10/2553bacterial identificationstrain-specificlactic acid bacteriaprobioticswhole genome sequencingcomparative genomics |
| spellingShingle | Despoina E. Kiousi Dimitrios M. Karadedos Anastasia Sykoudi Panagiotis Repanas Christina S. Kamarinou Anthoula A. Argyri Alex Galanis Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers Microorganisms bacterial identification strain-specific lactic acid bacteria probiotics whole genome sequencing comparative genomics |
| title | Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers |
| title_full | Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers |
| title_fullStr | Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers |
| title_full_unstemmed | Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers |
| title_short | Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers |
| title_sort | development of a multiplex pcr assay for efficient detection of two potential probiotic strains using whole genome based primers |
| topic | bacterial identification strain-specific lactic acid bacteria probiotics whole genome sequencing comparative genomics |
| url | https://www.mdpi.com/2076-2607/11/10/2553 |
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