Current strategies for mobilome research
Tue S Jørgensen1, Anne S Kiil1, Martin A Hansen1
1Section of Microbiology, Department of Biology, University of Copenhagen Copenhagen, Denmark.
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.
Insights
Mobile genetic elements (MGEs) drive bacterial evolution and antibiotic resistance. New metagenomic methods, including PacBio sequencing, help study these crucial elements in complex environments.
Area of Science:
- Microbiology
- Genetics
- Evolutionary Biology
Background:
- Mobile genetic elements (MGEs) are key drivers of bacterial evolution and adaptation.
- MGEs facilitate gene transfer, contributing significantly to the spread of antibiotic resistance.
- Traditional MGE studies focused on plasmids from individual isolates.
Purpose of the Study:
- To review recent approaches for studying entire plasmid pools from complex environments using metagenomic data.
- To highlight potential future developments and challenges in MGE research.
- To discuss the utility of PacBio long-read sequencing technology for MGE discovery.
Main Methods:
- Review of existing literature on MGE enrichment and sequencing techniques.
- Analysis of challenges in distinguishing MGEs from chromosomal DNA in metagenomic samples.
- Discussion of PacBio long-read sequencing for MGE identification.
Main Results:
- Metagenomic approaches offer powerful tools for studying MGEs in entire communities.
- Enrichment strategies are crucial for isolating plasmid DNA from complex samples.
- PacBio long-read sequencing shows promise for enhanced MGE discovery.
Conclusions:
- Advancements in sequencing technology enable comprehensive study of MGEs in microbial communities.
- Overcoming challenges in MGE separation is vital for understanding their role in bacterial adaptation and resistance.
- Future research should leverage advanced sequencing and enrichment methods for deeper insights into MGE dynamics.
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