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Microbial Genomics logo

Volume 6, Issue 10

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands Open Access

Abstract

Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82–94 % of chromosomes could be correctly recovered and binned, only 38–44 % of GIs and 1–29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0–45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , genomic islands , metagenome-assembled genomes , metagenomics and mobile genetic elements
Funding
This study was supported by the:
  • Natural Sciences and Engineering Research Council of Canada
    • Principle Award Recipient: Fiona S.L. Brinkman
  • Genome Canada
    • Principle Award Recipient: Robert G Beiko
  • Simon Fraser University (Award Distinguished Professorship)
    • Principle Award Recipient: Fiona S.L. Brinkman
  • Simon Fraser University (Award Omics and Data Sciences fellowship)
    • Principle Award Recipient: Wing Yin Venus Lau
  • Simon Fraser University (Award Omics and Data Sciences fellowship)
    • Principle Award Recipient: Kristen Gray
  • Simon Fraser University (Award Omics and Data Sciences fellowship)
    • Principle Award Recipient: Baofeng Jia
  • Natural Sciences and Engineering Research Council of Canada (Award Collaborative Research and Training Experience (CREATE) Bioinformatics scholarship)
    • Principle Award Recipient: Kristen Gray
  • Canadian Institutes of Health Research (Award Doctoral Scholarship)
    • Principle Award Recipient: Wing Yin Venus Lau
  • Donald Hill Family Fellowship
    • Principle Award Recipient: Finlay Maguire
  • Canadian Institutes of Health Research (Award Doctoral Scholarship)
    • Principle Award Recipient: Baofeng Jia
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2020-10-01
2024-04-24
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Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands
M Gen 6, e000436 (2020); https://doi.org/10.1099/mgen.0.000436
/content/journal/mgen/10.1099/mgen.0.000436
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