A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

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A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

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Bonnie Quigley

A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples

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Title: A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples
Author/Creator: Uyaguari-Diaz, M I | Chan, M | Chaban, Bonnie L | Croxen, M A | Finke, J F | Hill, J E | Peabody, M A | Rossum, T V | Suttle, C A | Brinkman, F S L | Isaac-Renton, J | Prystajecky, N A | Tang, P
Description: 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.
Relation: Microbiome / Vol. 4, No. 20
Relation: http://dx.doi.org/10.1186/s40168-016-0166-1
Year: 2016
Publisher: BioMed Central Ltd.
Subject: FoR 0602 (Ecology) | FoR 0605 (Microbiology) | FoR 1108 (Medical Microbiology) | amplicon sequencing | metagenomes | metagenomics | microbial fractions | microbiome | watersheds

Collection(s): Bonnie Quigley
Collection(s): Research Publications
Resource Type: Journal Article
Identifier: ISSN: 2049-2618
Rights: 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
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