MersV1, Main, Exploration, bibRecordById, PMC:3655615

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Identifieur interne : 002147 ( Main/Exploration ); précédent : 002146; suivant : 002148

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Auteurs : Bonnie L. Hurwitz [États-Unis] ; Li Deng [États-Unis] ; Bonnie T. Poulos [États-Unis] ; Matthew B. Sullivan [États-Unis]

Source :

Environmental Microbiology [ 1462-2912 ] ; 2013-05.

RBID : ISTEX:9B4EF5E4A6A9E8AD7AC5E36EEA2426EDE8EA65E1

Descripteurs français

KwdFr :
- Biodiversité, Eau de mer (virologie), Microbiologie de l'eau, Métagénomique, Protéines virales (analyse), Protéines virales (génétique), Reproductibilité des résultats, Virologie (), Virus (génétique), Virus (isolement et purification).
MESH :
- analyse : Protéines virales.
- génétique : Protéines virales, Virus.
- isolement et purification : Virus.
- virologie : Eau de mer.
Pascal (Inist)
- Communauté, Concentrat, Métagénome, Méthode, Océan, Virus.
MESH :
- Biodiversité, Microbiologie de l'eau, Métagénomique, Reproductibilité des résultats, Virologie.
Wicri :
- topic : Océan.

English descriptors

KwdEn :
- Biodiversity, Community, Concentrate, Metagenome, Metagenomics, Method, Ocean, Reproducibility of Results, Seawater (virology), Viral Proteins (analysis), Viral Proteins (genetics), Virology (methods), Virus, Viruses (genetics), Viruses (isolation & purification), Water Microbiology.
MESH :
- chemical , analysis : Viral Proteins.
- chemical , genetics : Viral Proteins.
- genetics : Viruses.
- isolation & purification : Viruses.
- methods : Virology.
- virology : Seawater.
Teeft :
- Appl environ microbiol, Biodiversity, Biol, Blackwell publishing, Breitbart, Cscl, Cscl dnase, Database, Deng, Dnase, Dnase cscl, Dnase sucrose, Ecology, Edta, Environ, Environ microbiol, Environmental microbiology, Experimental procedures, Fecl3, Fecl3 dnase, Fecl3 dnase cscl, Fecl3 dnase sucrose, Fecl3 precipitation, Genome, Genus levels, Hurwitz, Linker, Lter, Ltered, Marine viruses, Metagenome, Metagenomes, Metagenomic, Metagenomics, Microbial, Microbial genomes, Microbial metagenome, Microbiol, Microbiology, More variability, Nucleic, Nucleic acid, Other samples, Pfuturbo, Phage, Plo, Plos biol, Poulos, Precipitation, Proc natl acad, Prophage, Prophage regions, Protein clusters, Protein diversity, Qiagen sciences, Rare sequences, Rarefaction, Rarefaction analysis, Rarefaction curves, Replicates, Reproducibility of Results, Rohwer, Scripps pier, Seawater, Sequencing, Simap, Sucrose, Superkingdom, Takara, Taxon, Taxonomic, Total sequences, Triplicate, Triplicate metagenomes, Viral, Viral community, Viral community concentration, Viral concentration, Viral metagenomes, Water Microbiology, Williamson, Wommack.

Abstract

Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF‐concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3‐precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k‐mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF‐concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k‐mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture‐independent viral ecology studies.

Url:

DOI: 10.1111/j.1462-2920.2012.02836.x

Affiliations:

États-Unis

Le document en format XML

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<term>Metagenomics</term>
<term>Method</term>
<term>Ocean</term>
<term>Reproducibility of Results</term>
<term>Seawater (virology)</term>
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<term>Viral Proteins (genetics)</term>
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<term>Concentrat</term>
<term>Métagénome</term>
<term>Méthode</term>
<term>Océan</term>
<term>Virus</term>
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<keywords scheme="Teeft" xml:lang="en"><term>Appl environ microbiol</term>
<term>Biodiversity</term>
<term>Biol</term>
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<term>Cscl dnase</term>
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<term>Dnase cscl</term>
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<term>Edta</term>
<term>Environ</term>
<term>Environ microbiol</term>
<term>Environmental microbiology</term>
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<term>Fecl3 dnase</term>
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<term>Linker</term>
<term>Lter</term>
<term>Ltered</term>
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<term>Microbial metagenome</term>
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<term>Microbiology</term>
<term>More variability</term>
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<term>Qiagen sciences</term>
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<term>Rarefaction analysis</term>
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<term>Reproducibility of Results</term>
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<front><div type="abstract" xml:lang="en">Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF‐concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3‐precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k‐mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF‐concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k‐mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture‐independent viral ecology studies.</div>
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Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

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