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CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR

Matthew G. Links, View ORCID ProfileTim J. Dumonceaux, Luke McCarthy, Sean M. Hemmingsen, View ORCID ProfileEdward Topp, Alexia Comte, View ORCID ProfileJennifer R. Town
doi: https://doi.org/10.1101/492116
Matthew G. Links
1Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK Canada
2Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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Tim J. Dumonceaux
3Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
4Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
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Luke McCarthy
5National Research Council of Canada, Saskatoon, SK, Canada
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Sean M. Hemmingsen
5National Research Council of Canada, Saskatoon, SK, Canada
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Edward Topp
6Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
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Alexia Comte
3Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
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Jennifer R. Town
3Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, Canada
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  • For correspondence: jennifer.town@agr.gc.ca
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ABSTRACT

Molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. Unfortunately both amplicon-based and shotgun sequencing approaches have significant shortcomings that limit the ability to study microbiome dynamics. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. This new method generates a quantitative, pan-Domain community profile with significantly less expenditure and sequencing effort than a shotgun metagenomic sequencing approach. Molecular microbial profiles were compared for antibiotic-amended soil samples using CaptureSeq, shotgun metagenomics, and amplicon-based techniques. The CaptureSeq method generated a microbial profile that provided a much greater depth and sensitivity than shotgun metagenomic sequencing while simultaneously mitigating the bias effects associated with amplicon-based methods. The resulting community profile provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya). The applications of CaptureSeq are globally impactful and will facilitate highly accurate studies of host-microbiome interactions for environmental, crop, animal and human health.

DNA sequencing data associated with this work has been deposited at NCBI under BioProject PRJNA406970 and SRA deposits SRX3181274-SRX3181276 and SRX3187583-SRX3187601.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 13, 2018.
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CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR
Matthew G. Links, Tim J. Dumonceaux, Luke McCarthy, Sean M. Hemmingsen, Edward Topp, Alexia Comte, Jennifer R. Town
bioRxiv 492116; doi: https://doi.org/10.1101/492116
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CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR
Matthew G. Links, Tim J. Dumonceaux, Luke McCarthy, Sean M. Hemmingsen, Edward Topp, Alexia Comte, Jennifer R. Town
bioRxiv 492116; doi: https://doi.org/10.1101/492116

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