Assessing the Resolution of Methyltransferase-Mediated DNA Optical Mapping

D'huys, L.; Vitale, Raffaele; Ruppeka-Rupeika, E.; Goyvaerts, V.; Ruckebusch, Cyril; Hofkens, J.

Type de document :

Article dans une revue scientifique: Article original

DOI :

10.1021/acsomega.1c01381

PMID :

34471732

URL permanente :

http://hdl.handle.net/20.500.12210/109526

Titre :

Assessing the Resolution of Methyltransferase-Mediated DNA Optical Mapping

Auteur(s) :

D'huys, L. [Auteur]
Catholic University of Leuven = Katholieke Universiteit Leuven [KU Leuven]
Vitale, Raffaele [Auteur]
Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 [LASIRE]
Ruppeka-Rupeika, E. [Auteur]
Catholic University of Leuven = Katholieke Universiteit Leuven [KU Leuven]
Goyvaerts, V. [Auteur]
Catholic University of Leuven = Katholieke Universiteit Leuven [KU Leuven]
Ruckebusch, Cyril [Auteur]

Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516
Hofkens, J. [Auteur]
Catholic University of Leuven = Katholieke Universiteit Leuven [KU Leuven]

Titre de la revue :

Acs Omega

Nom court de la revue :

ACS Omega

Numéro :

Pagination :

21276–21283

Date de publication :

2021-09-08

ISSN :

2470-1343

Discipline(s) HAL :

Chimie/Chimie théorique et/ou physique

Résumé en anglais : [en]

Interest in the human microbiome is growing and has been, for the past decade, leading to new insights into disease etiology and general human biology. Stimulated by these advances and in a parallel trend, new DNA sequencing ...
Lire la suite >Interest in the human microbiome is growing and has been, for the past decade, leading to new insights into disease etiology and general human biology. Stimulated by these advances and in a parallel trend, new DNA sequencing platforms have been developed, radically expanding the possibilities in microbiome research. While DNA sequencing plays a pivotal role in this field, there are some technological hurdles that are yet to be overcome. Targeting of the 16S rRNA gene with amplicon sequencing, for instance, is frequently used for sample composition profiling due to its short sample-to-result time and low cost, which counterbalance its low resolution (genus to species level). On the other hand, more comprehensive methods, namely, whole-genome sequencing (WGS) and shallow shotgun sequencing, are capable of yielding single-gene- and functional-level resolution at a higher cost and much higher sample processing time. It goes without saying that the existing gap between these two types of approaches still calls for the development of a fast, robust, and low-cost analytical platform. In search of the latter, we investigated the taxonomic resolution of methyltransferase-mediated DNA optical mapping and found that strain-level identification can be achieved with both global and whole-genome analyses as well as using a unique identifier (UI) database. In addition, we demonstrated that UI selection in DNA optical mapping, unlike variable region selection in 16S amplicon sequencing, is not limited to any genomic location, explaining the increase in resolution. This latter aspect was highlighted by SCCmec typing in methicillin-resistant Staphylococcus aureus (MRSA) using a simulated data set. In conclusion, we propose DNA optical mapping as a method that has the potential to be highly complementary to current sequencing platforms.Lire moins >

Langue :

Anglais

Audience :

Internationale

Vulgarisation :

Non

Établissement(s) :

Université de Lille
CNRS

Collections :

Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516

Date de dépôt :

2024-02-28T22:37:43Z
2024-03-15T13:01:01Z

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Ce document est diffusé sous licence Attribution-NonCommercial-NoDerivs 3.0 United States

Numéro de version	Lien	Date de modification
2	20.500.12210/109526*	2024-03-15T12:57:17Z
1	20.500.12210/109526.1	2024-02-28T22:37:43Z

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