Journal article
A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples
Microbiome, Vol.4, 20
2016
Abstract
Background: Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. Results: We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. Conclusion: This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia. © 2016 Uyaguari-Diaz et al.
Details
- Title
- A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples
- Authors
- M I Uyaguari-Diaz (Author) - British Columbia Centre for Disease Control, CanadaM Chan (Author) - British Columbia Centre for Disease Control, CanadaBonnie L Chaban (Author) - Imperial College London, United KingdomM A Croxen (Author) - British Columbia Centre for Disease Control, CanadaJ F Finke (Author) - University of British Columbia, CanadaJ E Hill (Author) - University of Saskatchewan, CanadaM A Peabody (Author) - Simon Fraser University, CanadaT V Rossum (Author) - Simon Fraser University, CanadaC A Suttle (Author) - University of British Columbia, CanadaF S L Brinkman (Author) - Simon Fraser University, CanadaJ Isaac-Renton (Author) - British Columbia Centre for Disease Control, CanadaN A Prystajecky (Author) - British Columbia Centre for Disease Control, CanadaP Tang (Author) - Sidra Medical and Research Center, Qatar
- Publication details
- Microbiome, Vol.4, 20; 19
- Publisher
- BioMed Central Ltd.
- Date published
- 2016
- DOI
- 10.1186/s40168-016-0166-1
- ISSN
- 2049-2618
- Copyright note
- Copyright © 2016 Uyaguari-Diaz et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
- Organisation Unit
- University of the Sunshine Coast, Queensland; Thompson Institute; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99451031502621
- Output Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web Of Science research areas
- Microbiology