TY - JOUR
T1 - A Novel and Direct Metamobilome Approach improves the Detection of Larger-sized Circular Elements across Kingdoms
AU - Alanin, Katrine Skov
AU - Joergensen, Tue Sparholt
AU - Browne, Patrick Denise
AU - Petersen, Bent
AU - Riber, Leise
AU - Kot, Witold Piotr
AU - Hansen, Lars Hestbjerg
PY - 2019
Y1 - 2019
N2 - Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, mobilomes are not studied to the same extent as bacterial genomes, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous mobilome publications. In this study, we show that MDA is detrimental for the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.
AB - Mobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, mobilomes are not studied to the same extent as bacterial genomes, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous mobilome publications. In this study, we show that MDA is detrimental for the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.
U2 - 10.1101/761098
DO - 10.1101/761098
M3 - Journal article
JO - bioRxiv
JF - bioRxiv
M1 - 761098
ER -
