Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis
The microbial community in Kawah Hujan, Kamojang, West Java, Indonesia, was analyzed using 16S-rRNA-gene-sequencing combining with denaturing-gradient-gel electrophoresis (DGGE) technique. Two different cell lysis methods, enzymatic-based, and physical treatment-based DNA extraction, were used to is...
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| Format: | Article |
| Language: | English |
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Indonesian Society for Microbiology
2010-03-01
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| Series: | Microbiology Indonesia |
| Subjects: | |
| Online Access: | https://jurnal.permi.or.id/index.php/mionline/article/view/28 |
| _version_ | 1818390961070276608 |
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| author | HENI YOHANDINI FIDA MADAYANTI PINGKAN ADITIAWATI . AKHMALOKA |
| author_facet | HENI YOHANDINI FIDA MADAYANTI PINGKAN ADITIAWATI . AKHMALOKA |
| author_sort | HENI YOHANDINI |
| collection | DOAJ |
| description | The microbial community in Kawah Hujan, Kamojang, West Java, Indonesia, was analyzed using 16S-rRNA-gene-sequencing combining with denaturing-gradient-gel electrophoresis (DGGE) technique. Two different cell lysis methods, enzymatic-based, and physical treatment-based DNA extraction, were used to isolate chromosomal DNA for 16S rDNA gene-fragment amplification. The DGGE profiles showed some differences in banding pattern that were obtained from both cell lysis methods. The DNA sequence analysis of the individual DGGE bands revealed that most of the band sequences obtained by physical treatment were close to 16S rRNA gene fragments from the bacterial domain, while most of band sequences performed by enzymatic method had high homology with 16S rRNA gene fragments from archaeal domain. Further analysis of the sequences from both methods performed by comparisons with the Ribosomal Database Project showed that some of DGGE sequences from Kawah Hujan consisted unique 16S rDNA sequences. |
| first_indexed | 2024-12-14T05:05:56Z |
| format | Article |
| id | doaj.art-dd30573e4f524c42a71f090c74c0f443 |
| institution | Directory Open Access Journal |
| issn | 1978-3477 2087-8575 |
| language | English |
| last_indexed | 2024-12-14T05:05:56Z |
| publishDate | 2010-03-01 |
| publisher | Indonesian Society for Microbiology |
| record_format | Article |
| series | Microbiology Indonesia |
| spelling | doaj.art-dd30573e4f524c42a71f090c74c0f4432022-12-21T23:16:06ZengIndonesian Society for MicrobiologyMicrobiology Indonesia1978-34772087-85752010-03-012110.5454/mi.2.1.624Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping AnalysisHENI YOHANDINIFIDA MADAYANTIPINGKAN ADITIAWATI. AKHMALOKAThe microbial community in Kawah Hujan, Kamojang, West Java, Indonesia, was analyzed using 16S-rRNA-gene-sequencing combining with denaturing-gradient-gel electrophoresis (DGGE) technique. Two different cell lysis methods, enzymatic-based, and physical treatment-based DNA extraction, were used to isolate chromosomal DNA for 16S rDNA gene-fragment amplification. The DGGE profiles showed some differences in banding pattern that were obtained from both cell lysis methods. The DNA sequence analysis of the individual DGGE bands revealed that most of the band sequences obtained by physical treatment were close to 16S rRNA gene fragments from the bacterial domain, while most of band sequences performed by enzymatic method had high homology with 16S rRNA gene fragments from archaeal domain. Further analysis of the sequences from both methods performed by comparisons with the Ribosomal Database Project showed that some of DGGE sequences from Kawah Hujan consisted unique 16S rDNA sequences.https://jurnal.permi.or.id/index.php/mionline/article/view/28Kamojangmicrobial diversity16S rRNAdenaturing-gradient-gel electrophoresis |
| spellingShingle | HENI YOHANDINI FIDA MADAYANTI PINGKAN ADITIAWATI . AKHMALOKA Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis Microbiology Indonesia Kamojang microbial diversity 16S rRNA denaturing-gradient-gel electrophoresis |
| title | Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis |
| title_full | Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis |
| title_fullStr | Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis |
| title_full_unstemmed | Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis |
| title_short | Cell Lysis Method Affects Assessment of Microbial Diversity Based on Ribotyping Analysis |
| title_sort | cell lysis method affects assessment of microbial diversity based on ribotyping analysis |
| topic | Kamojang microbial diversity 16S rRNA denaturing-gradient-gel electrophoresis |
| url | https://jurnal.permi.or.id/index.php/mionline/article/view/28 |
| work_keys_str_mv | AT heniyohandini celllysismethodaffectsassessmentofmicrobialdiversitybasedonribotypinganalysis AT fidamadayanti celllysismethodaffectsassessmentofmicrobialdiversitybasedonribotypinganalysis AT pingkanaditiawati celllysismethodaffectsassessmentofmicrobialdiversitybasedonribotypinganalysis AT akhmaloka celllysismethodaffectsassessmentofmicrobialdiversitybasedonribotypinganalysis |