About: Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

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About: Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
Creator	Matthijnssens, Jelle Conceição-Neto, Nádia Van Ranst, Marc Maes, Piet Heylen, Elisabeth Lefrère, Hanne Zeller, Mark Beller, Leen Deboutte, Ward De Bruyn, Pieter Lavigne, Rob Kwe Yinda, Claude
Source	Medline; PMC
abstract	A major limitation for better understanding the role of the human gut virome in health and disease is the lack of validated methods that allow high throughput virome analysis. To overcome this, we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome (containing nine highly diverse viruses) and a bacterial mock-community (containing four faecal bacterial species) using quantitative PCR and next-generation sequencing. This resulted in an optimised protocol that was able to recover all viruses present in the mock-virome and strongly alters the ratio of viral versus bacterial and 16S rRNA genetic material in favour of viruses (from 43.2% to 96.7% viral reads and from 47.6% to 0.19% bacterial reads). Furthermore, our study indicated that most of the currently used virome protocols, using small filter pores and/or stringent centrifugation conditions may have largely overlooked large viruses present in viromes. We propose NetoVIR (Novel enrichment technique of VIRomes), which allows for a fast, reproducible and high throughput sample preparation for viral metagenomics studies, introducing minimal bias. This procedure is optimised mainly for faecal samples, but with appropriate concentration steps can also be used for other sample types with lower initial viral loads.
has issue date	2015-11-12(xsd:dateTime)
bibo:doi	10.1038/srep16532
bibo:pmid	26559140
has license	cc-by
sha1sum (hex)	d0ad5a9116068caa5f78a95f8141a2a811662793
schema:url	https://doi.org/10.1038/srep16532
resource representing a document's title	Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
has PubMed Central identifier	PMC4642273
has PubMed identifier	26559140
schema:publication	Sci Rep
resource representing a document's body	covid:d0ad5a9116068caa5f78a95f8141a2a811662793#body_text
is schema:about of	named entity 'viruses' named entity 'PROTOCOL' named entity 'VIRAL' named entity 'BACTERIAL' named entity 'FILTRATION' covid:arg/d0ad5a9116068caa5f78a95f8141a2a811662793 named entity 'STUDY' named entity 'HOMOGENISATION' named entity 'RATIO' named entity 'MOST OF' named entity 'SAMPLES' named entity 'METHODS' named entity 'SMALL' named entity 'FAECAL' named entity 'SAMPLE' named entity 'ANALYSIS' named entity 'DIVERSE' named entity 'APPROPRIATE' named entity 'USING' named entity 'VALIDATED' named entity 'CONCENTRATION' named entity 'CENTRIFUGATION' named entity 'CURRENTLY' named entity 'ENRICHMENT' named entity 'STEPS' named entity '16S RRNA' named entity 'INDICATED' named entity 'METAGENOMICS' named entity 'VIRUSES' named entity 'BUT' named entity 'TYPES' named entity 'PROTOCOL' named entity 'BETTER' named entity 'READS' named entity 'MAY HAVE' named entity 'CHLOROFORM' named entity 'PREPARATION PROCEDURES' named entity 'SAMPLE PREPARATION' named entity 'LIMITATION' named entity 'HIGHLY' named entity 'TREATMENT' named entity 'FILTER' named entity 'STUDIES' named entity 'USED' named entity 'PROTOCOLS' named entity 'LACK' named entity 'AMPLIFICATION' named entity 'QUANTITATIVE' named entity 'HUMAN' named entity 'OUR' named entity 'NEXT-GENERATION SEQUENCING' named entity 'CONDITIONS' named entity 'BIAS' named entity 'TECHNIQUE' named entity 'LARGE' named entity 'FAST' named entity 'PRESENT' named entity 'QUANTITATIVE PCR' named entity 'HEALTH AND DISEASE' named entity 'GUT' named entity '0.19' named entity 'ROLE' named entity 'PROCEDURE' named entity 'LOWER' named entity 'METAGENOMICS' named entity 'RANDOM' named entity 'INITIAL' named entity 'COMMUNITY' named entity 'SAMPLE PREPARATION' named entity 'VIRAL'

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