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Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights
  • Mason Stothart,
  • Philip McLoughlin,
  • Jocelyn Poissant
Mason Stothart
University of Calgary

Corresponding Author:[email protected]

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Philip McLoughlin
University of Saskatchewan
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Jocelyn Poissant
University of Calgary
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Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. We evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the fecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional versus high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective lab methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon dataset. Unlike amplicon data, we demonstrate how shallow shotgun metagenomic data also provided useful insights about microbiome functional potential which support previously hypothesized diet effects in this study system.
26 Mar 2022Submitted to Molecular Ecology Resources
08 Apr 2022Submission Checks Completed
08 Apr 2022Assigned to Editor
12 Apr 2022Reviewer(s) Assigned
01 Jun 2022Review(s) Completed, Editorial Evaluation Pending
20 Jun 2022Editorial Decision: Revise Minor
17 Jul 2022Review(s) Completed, Editorial Evaluation Pending
17 Jul 20221st Revision Received
18 Jul 2022Reviewer(s) Assigned
09 Sep 2022Editorial Decision: Accept
26 Sep 2022Published in Molecular Ecology Resources. 10.1111/1755-0998.13713