Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities
The aim of this study is to optimize molecular detection and quantification methods of probiotic bacteria in complex microbial communities that have long been difficult for traditional culture-based methods. Traditional and real-time PCR were optimized to detect and quantify Lactobacillus spp. and B...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Academic Journals
2010
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| Online Access: | http://psasir.upm.edu.my/id/eprint/13928/ http://psasir.upm.edu.my/id/eprint/13928/1/13928.pdf |
| _version_ | 1848842251465129984 |
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| author | Abdulamir, Ahmed Sahib Yoke, T. S. Nordin, Noordiana Abu Bakar, Fatimah |
| author_facet | Abdulamir, Ahmed Sahib Yoke, T. S. Nordin, Noordiana Abu Bakar, Fatimah |
| author_sort | Abdulamir, Ahmed Sahib |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | The aim of this study is to optimize molecular detection and quantification methods of probiotic bacteria in complex microbial communities that have long been difficult for traditional culture-based methods. Traditional and real-time PCR were optimized to detect and quantify Lactobacillus spp. and Bifidobacterium spp. in complex microbial community. Fish and shrimp sauce were used as a model for complex microbial community. Directly form samples, 4 DNA extraction methods, primers specificity, PCR, and real-time PCR procedures were optimized, tested in comparison with samples, enriched bacteria and related standard bacterial strains, E. coli, Bacteroides, Enterococcus and Salmonella. Results showed that extracted genomic DNA using Wizard® Genomic DNA Purification Kit showed the highest yield, quality and performance. Moreover, the specificity of the primer set specific for Lactobacillus spp. and Bifidobacterium spp. was checked and found highly specific. The sensitivity of real-time PCR was higher than the conventional PCR and its quantifying potential is very precise for the detection and quantification of Lactobacillus spp. but not Bifidobacterium spp. which was absent in the tested samples. In conclusion, PCR and real-time PCR assays could be used very efficiently in quantifying and detecting Lactobacillus spp. that are present in very PCR-suppressive and complex microbial environment. |
| first_indexed | 2025-11-15T07:56:10Z |
| format | Article |
| id | upm-13928 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T07:56:10Z |
| publishDate | 2010 |
| publisher | Academic Journals |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-139282017-11-09T04:32:34Z http://psasir.upm.edu.my/id/eprint/13928/ Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities Abdulamir, Ahmed Sahib Yoke, T. S. Nordin, Noordiana Abu Bakar, Fatimah The aim of this study is to optimize molecular detection and quantification methods of probiotic bacteria in complex microbial communities that have long been difficult for traditional culture-based methods. Traditional and real-time PCR were optimized to detect and quantify Lactobacillus spp. and Bifidobacterium spp. in complex microbial community. Fish and shrimp sauce were used as a model for complex microbial community. Directly form samples, 4 DNA extraction methods, primers specificity, PCR, and real-time PCR procedures were optimized, tested in comparison with samples, enriched bacteria and related standard bacterial strains, E. coli, Bacteroides, Enterococcus and Salmonella. Results showed that extracted genomic DNA using Wizard® Genomic DNA Purification Kit showed the highest yield, quality and performance. Moreover, the specificity of the primer set specific for Lactobacillus spp. and Bifidobacterium spp. was checked and found highly specific. The sensitivity of real-time PCR was higher than the conventional PCR and its quantifying potential is very precise for the detection and quantification of Lactobacillus spp. but not Bifidobacterium spp. which was absent in the tested samples. In conclusion, PCR and real-time PCR assays could be used very efficiently in quantifying and detecting Lactobacillus spp. that are present in very PCR-suppressive and complex microbial environment. Academic Journals 2010-03-08 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/13928/1/13928.pdf Abdulamir, Ahmed Sahib and Yoke, T. S. and Nordin, Noordiana and Abu Bakar, Fatimah (2010) Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities. African Journal of Biotechnology, 9 (10). art. no. B0589C517656. pp. 1481-1492. ISSN 1684–5315 http://www.academicjournals.org/journal/AJB/article-abstract/B0589C517656 |
| spellingShingle | Abdulamir, Ahmed Sahib Yoke, T. S. Nordin, Noordiana Abu Bakar, Fatimah Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title | Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title_full | Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title_fullStr | Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title_full_unstemmed | Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title_short | Detection and quantification of probiotic bacteria using optimized DNA extraction, traditional and real-time PCR methods in complex microbial communities |
| title_sort | detection and quantification of probiotic bacteria using optimized dna extraction, traditional and real-time pcr methods in complex microbial communities |
| url | http://psasir.upm.edu.my/id/eprint/13928/ http://psasir.upm.edu.my/id/eprint/13928/ http://psasir.upm.edu.my/id/eprint/13928/1/13928.pdf |