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Protocols

VIROME specifications

Information


Unique identifier OMICS_01506
Name VIROME
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for VIROME

VIROME citations

 (23)
call_split

Exploring Viral Diversity in a Unique South African Soil Habitat

2018
Sci Rep
PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0
call_split See protocol

[…] e processed reads were assembled de novo using CLC Genomics Workbench version 6.0.1 using the default settings. Reads and contigs were uploaded to the MetaVir (http://metavir-meb.univ-bpclermont.fr), VIROME (http://virome.dbi.udel.edu/) and MG-RAST (http://metagenomics.anl.gov/) servers for virus diversity estimations. The viromes were uploaded in 2015 and analysed in 2017. The taxonomic compositi […]

library_books

Viral communities of the human gut: metagenomic analysis of composition and dynamics

2017
Mob DNA
PMCID: 5627405
PMID: 29026445
DOI: 10.1186/s13100-017-0095-y

[…] rs. Integration of the phage genome into the bacterial genome can take place via either phage-encoded integrases (shiga toxin) [] or by hijacking host cell recombination machinery (cholera toxin) []. Virome studies are just beginning to report the global frequency of occurrence of such toxin genes in different environments []. Other gene types are also known to influence human health [].Less clear […]

library_books

Review article: the human intestinal virome in health and disease

2017
PMCID: 5656937
PMID: 28869283
DOI: 10.1111/apt.14280

[…] the faeces of the 1‐week‐old infant. Similar to adult DNA viral metagenomes, siphophage and prophage sequences predominated. Eight viral genotypes were predicted to be present in the infant's faecal virome, with the most abundant viral genotype contributing 43.6% to the total. The low diversity of the infant faecal virome correlated well with the known low diversity of the faecal bacterial assemb […]

library_books

The In Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome

2017
MBio
PMCID: 5550749
PMID: 28790203
DOI: 10.1128/mBio.00709-17

[…] o FLX plus chemistry (454 Life Sciences) plates, and phage DNA was sequenced on a Roche GS-FLX instrument with one titanium chemistry plate. The microbial metatranscriptome, microbial metagenome, and virome were all used to form a composite assembly, and an assembly of the phage sequences alone was also completed. ORFs in contigs were predicted, sequences were mapped to ORFs and counted (), and OR […]

library_books

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology

2017
PMCID: 5649160
PMID: 28731469
DOI: 10.1038/ismej.2017.102

[…] This survey of virioplankton chaperonin genes was facilitated by virome sequence data from a variety of marine locations, coupled with the SERC virome that was deeply sequenced and included long PacBio sequence reads. These data provided long contigs for examining […]

call_split

Environmental drivers of viral community composition in Antarctic soils identified by viromics

2017
Microbiome
PMCID: 5518109
PMID: 28724405
DOI: 10.1186/s40168-017-0301-7
call_split See protocol

[…] ome hg18 (GRCh38, UCSC Genome Browser), and an Escherichia coli reference genome (strain C43(DE3), GenBank accession number CP011938) to remove non-soil virus sequences. De novo assembly of each soil virome was performed with the assembly and mapping algorithm using default parameters for Ion Torrent data. Fourteen assembled viromes were uploaded to the MetaVir server (http://metavir-meb.univ-bpcl […]

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VIROME institution(s)
Delaware Biotechnology Institute, University of Delaware, Newark, DE

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