An improved direct metamobilome approach increases the detection of larger-sized circular elements across kingdoms

Katrine Wacenius Skov Alanin, Tue Sparholt Jørgensen, Patrick Denis Browne, Bent Petersen, Leise Riber, Witold Kot*, Lars Hestbjerg Hansen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate genetic diversity. MGEs serve as a vast communal gene pool and include DNA elements such as plasmids and bacteriophages (phages) among others. These mobile DNA elements represent a human health risk as they can introduce new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting environmental circular MGEs, referred to as metamobilomes, may broaden our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomics is affected by a severe bias towards small circular elements, introduced by multiple displacement amplification (MDA). MDA is typically used to overcome limiting DNA quantities after the removal of non-circular DNA during library preparations. By examining the relationship between sequencing coverage and the size of circular MGEs in paired metamobilome datasets with and without MDA, we show that larger circular elements are lost when using MDA. This study is the first to systematically demonstrate that MDA is detrimental to detecting larger-sized plasmids if small plasmids are present. It is also the first to show that MDA can be omitted when using enzyme-based DNA fragmentation and PCR in library preparation kits such as Nextera XT® from Illumina.

Original languageEnglish
Article number102576
JournalPlasmid
Volume115
ISSN0147-619X
DOIs
Publication statusPublished - May 2021

Keywords

  • ICEs
  • IS-elements
  • Metamobilomes
  • Mobile genetic elements (MGEs)
  • Plasmids
  • Sequencing libraries

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