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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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