Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis
Samo za registrovane korisnike
2010
Autori
Salonen, AnneNikkila, Janne
Jalanka-Tuovinen, Jonna
Immonen, Outi
Rajilić-Stojanović, Mirjana
Kekkonen, Riina A.
Palva, Airi
de Vos, Willem M.
Članak u časopisu (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations gt 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, in...cluding Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.
Ključne reči:
Intestinal microbiota / DNA extraction / 16S rRNA / MicroarrayIzvor:
Journal of Microbiological Methods, 2010, 81, 2, 127-134Izdavač:
- Elsevier Science Bv, Amsterdam
Finansiranje / projekti:
- Finnish Funding Agency for Technology and Innovation (TEKES)Finnish Funding Agency for Technology & Innovation (TEKES) [40274/06]
DOI: 10.1016/j.mimet.2010.02.007
ISSN: 0167-7012
PubMed: 20171997
WoS: 000277949900007
Scopus: 2-s2.0-77951977802
Institucija/grupa
Tehnološko-metalurški fakultetTY - JOUR AU - Salonen, Anne AU - Nikkila, Janne AU - Jalanka-Tuovinen, Jonna AU - Immonen, Outi AU - Rajilić-Stojanović, Mirjana AU - Kekkonen, Riina A. AU - Palva, Airi AU - de Vos, Willem M. PY - 2010 UR - http://TechnoRep.tmf.bg.ac.rs/handle/123456789/1694 AB - Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations gt 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories. PB - Elsevier Science Bv, Amsterdam T2 - Journal of Microbiological Methods T1 - Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis EP - 134 IS - 2 SP - 127 VL - 81 DO - 10.1016/j.mimet.2010.02.007 ER -
@article{ author = "Salonen, Anne and Nikkila, Janne and Jalanka-Tuovinen, Jonna and Immonen, Outi and Rajilić-Stojanović, Mirjana and Kekkonen, Riina A. and Palva, Airi and de Vos, Willem M.", year = "2010", abstract = "Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations gt 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.", publisher = "Elsevier Science Bv, Amsterdam", journal = "Journal of Microbiological Methods", title = "Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis", pages = "134-127", number = "2", volume = "81", doi = "10.1016/j.mimet.2010.02.007" }
Salonen, A., Nikkila, J., Jalanka-Tuovinen, J., Immonen, O., Rajilić-Stojanović, M., Kekkonen, R. A., Palva, A.,& de Vos, W. M.. (2010). Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. in Journal of Microbiological Methods Elsevier Science Bv, Amsterdam., 81(2), 127-134. https://doi.org/10.1016/j.mimet.2010.02.007
Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilić-Stojanović M, Kekkonen RA, Palva A, de Vos WM. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. in Journal of Microbiological Methods. 2010;81(2):127-134. doi:10.1016/j.mimet.2010.02.007 .
Salonen, Anne, Nikkila, Janne, Jalanka-Tuovinen, Jonna, Immonen, Outi, Rajilić-Stojanović, Mirjana, Kekkonen, Riina A., Palva, Airi, de Vos, Willem M., "Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis" in Journal of Microbiological Methods, 81, no. 2 (2010):127-134, https://doi.org/10.1016/j.mimet.2010.02.007 . .