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Virtual Metagenome specifications

Information


Unique identifier OMICS_17893
Name Virtual Metagenome
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Shujiro Okuda

Publication for Virtual Metagenome

Virtual Metagenome citations

 (5)
library_books

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity

2018
Front Microbiol
PMCID: 5768659
PMID: 29375532
DOI: 10.3389/fmicb.2017.02670

[…] ing the 97% similarity implemented in QIIME v. 1.8.0 (). We reconstructed and predicted the functional contribution of each OTU member by mapping 16S sequences with their nearest reference genome. A “virtual” metagenome with gene content abundance was then generated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Ortholog. The abundance of each KEGG Orthologs category was presented in a K […]

call_split

Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift

2017
Front Microbiol
PMCID: 5566599
PMID: 28871246
DOI: 10.3389/fmicb.2017.01585
call_split See protocol

[…] Then, the OTU abundance was normalized automatically using 16S rRNA gene copy numbers from the reference bacterial and archaeal genomes in Integrated Microbial Genomes (IMG) database (). Finally, a ‘virtual’ metagenome of clusters of orthologous groups (COGs) with their abundances were produced based on the previous normalized OTU table using the default settings in PICRUSt (; ). […]

library_books

A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data

2017
Virus Evol
PMCID: 5544889
PMID: 28798873
DOI: 10.1093/ve/vex016

[…] ate of viral discovery, but have focused on clinical and environmental samples collected for this purpose (; ; ; ). In this paper, we repurposed host genome databases by mining them collectively as a virtual metagenome, adding to a growing trend in searching for viruses in this way (; ; ). This approach arises from the recognition that paleovirology and viral metagenomics share an overlapping set […]

library_books

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales

2016
Nat Commun
PMCID: 4899628
PMID: 27270557
DOI: 10.1038/ncomms11833

[…] eny relative to all bacteria or archaea with sequenced genomes. These per genome estimates are then combined, taking into account 16S rRNA copy number variation, to estimate a functional profile (or ‘virtual metagenome') for a microbial community based on the information available in all sequenced genomes. The resulting metagenomes have been used in recent analyses of human and environmental micro […]

call_split

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment

2015
Genome Med
PMCID: 4499914
PMID: 26170900
DOI: 10.1186/s13073-015-0177-8
call_split See protocol

[…] n two degrees of separation from Providencia or Fusobacterium with absolute correlations of 0.05 or more were visualized using Cytoscape v.3.1.0 [].The PICRUSt v.1.0.0 pipeline was used to generate a virtual metagenome using the OTU table containing raw counts generated in the previous analyses by QIIME [, , ]. Pathways and enzymes were assigned using the Kyoto Encyclopedia of Genes and Genomes (K […]

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Virtual Metagenome institution(s)
Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga, Japan; Graduate School of Science and Engineering, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga, Japan; Graduate School of Information Science and Technology, Hokkaido University, Kita, Nishi, Kita-ku, Sapporo, Hokkaido, Japan
Virtual Metagenome funding source(s)
This work was supported by grant-in-aid for Young Scientists from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT).

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