title: Current strategies for mobilome research.
abstract: Mobile genetic elements (MGEs) are pivotal for bacterial evolution and adaptation, allowing shuﬄing of genes even between distantly related bacterial species. The study of these elements is biologically interesting as the mode of genetic propagation is kaleidoscopic and important, as MGEs are the main vehicles of the increasing bacterial antibiotic resistance that causes thousands of human deaths each year. The study of MGEs has previously focused on plasmids from individual isolates, but the revolution in sequencing technology has allowed the study of mobile genomic elements of entire communities using metagenomic approaches. The problem in using metagenomic sequencing for the study of MGEs is that plasmids and other mobile elements only comprise a small fraction of the total genetic content that are difficult to separate from chromosomal DNA based on sequence alone. The distinction between plasmid and chromosome is important as the mobility and regulation of genes largely depend on their genetic context. Several different approaches have been proposed that specifically enrich plasmid DNA from community samples. Here, we review recent approaches used to study entire plasmid pools from complex environments, and point out possible future developments for and pitfalls of these approaches. Further, we discuss the use of the PacBio long-read sequencing technology for MGE discovery.
authors: Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
authors: Tue S
authors: TS
authors: Jørgensen
authors: Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
authors: Anne S
authors: AS
authors: Kiil
authors: Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
authors: Martin A
authors: MA
authors: Hansen
authors: Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
authors: Søren J
authors: SJ
authors: Sørensen
authors: Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark ; Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University Roskilde, Denmark.
authors: Lars H
authors: LH
authors: Hansen
keywords: MGE; PacBio; horizontal gene transfer; metagenomics; mobile genetic elements; mobilome; plasmid; plasmidome
references: Clin Microbiol Infect. 2012 Jul;18 Suppl 4:5-7
references: 22647039
references: Nat Methods. 2007 Jan;4(1):55-61
references: 17128268
references: Environ Microbiol. 2009 Feb;11(2):349-59
references: 19196269
references: Science. 2009 Nov 6;326(5954):858-61
references: 19892985
references: Genome Res. 2008 May;18(5):821-9
references: 18349386
references: Bioinformatics. 2012 Jun 1;28(11):1420-8
references: 22495754
references: J Microbiol Methods. 2013 Nov;95(2):272-9
references: 24055388
references: Appl Environ Microbiol. 1996 Jul;62(7):2621-8
references: 8779598
references: J Biomol Tech. 2005 Jun;16(2):125-33
references: 16030319
references: Sci Transl Med. 2014 Sep 17;6(254):254ra126
references: 25232178
references: Genome Res. 2001 Jun;11(6):1095-9
references: 11381035
references: Appl Environ Microbiol. 2014 Jul;80(13):4012-20
references: 24771027
references: Nat Biotechnol. 2014 Aug;32(8):822-8
references: 24997787
references: Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17332-6
references: 16286637
references: Genome Res. 2012 Jan;22(1):125-33
references: 22090378
references: Environ Microbiol. 2012 Feb;14(2):453-66
references: 22059529
references: PLoS One. 2014 Aug 12;9(8):e104405
references: 25116381
references: Biotechniques. 2012 Dec;53(6):365-72
references: 23227987
references: ISME J. 2013 Jun;7(6):1173-86
references: 23407308
references: BMC Bioinformatics. 2008 Sep 19;9:386
references: 18803844
references: Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5452-7
references: 22431592
references: Appl Environ Microbiol. 2000 Nov;66(11):4854-62
references: 11055935
references: PLoS One. 2014 Feb 04;9(2):e87924
references: 24503942
references: Plasmid. 2006 Jul;56(1):1-10
references: 16472859
references: Nat Rev Microbiol. 2005 Sep;3(9):700-10
references: 16138098