Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies

Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies. Rehner, J., Schmartz , G. P., Groeger, L., Dastbaz, J., Ludwig, N., Hannig, M., Rupf, S., Seitz, B., Flockerzi, E., Berger, T., Reichert, M. C., Krawczyk, M., Meese, E., Herr, C., Bals, R., Becker, S. L., Keller, A., & Müller, R. Genomics, Proteomics & Bioinformatics, 06, 2022.

Paper doi abstract bibtex

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across data sets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of specimen type and DNA extraction, 20 GB metagenomic data were generated using short-read sequencing. While profiles of the specimen type showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kit. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 GB of sequencing data are required to achieve sufficient resolution, but DNA-based identification was superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

@article{REHNER2022,
	title = {Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies},
	journal = {Genomics, Proteomics & Bioinformatics},
	year = {2022},
	issn = {1672-0229},
	month = {06},
	doi = {10.1016/j.gpb.2022.05.006},
	url = {https://www.sciencedirect.com/science/article/pii/S1672022922000729},
	author = {Rehner, Jacqueline and Schmartz , Georges Pierre and Groeger, Laura and Dastbaz, Jan and Ludwig, Nicole and Hannig, Matthias and Rupf, Stefan and Seitz, Berthold and Flockerzi, Elias and Berger, Tim and Reichert, Matthias Christian and Krawczyk, Marcin and Meese, Eckart and Herr, Christian and Bals, Robert and Becker, Sören L. and Keller, Andreas and Müller, Rolf },
	keywords = {Whole-genome analysis, Comparative genomics, Short-read sequencing, Long-read sequencing, DNA extraction, Metagenomics},
	abstract = {High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across data sets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of specimen type and DNA extraction, 20 GB metagenomic data were generated using short-read sequencing. While profiles of the specimen type showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kit. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 GB of sequencing data are required to achieve sufficient resolution, but DNA-based identification was superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.}
}

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