TY  - 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 . .