| Open resource metagenomics: a model for sharing metagenomic libraries. | |
| | |
MedLine Citation:
|
PMID: 22180823 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
|
Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. |
| | |
Authors:
|
J D Neufeld; K Engel; J Cheng; G Moreno-Hagelsieb; D R Rose; T C Charles |
Related Documents
:
|
7579183 - Absence of psac subunit allows assembly of photosystem i core but prevents the binding ... 18762903 - Identification of cytoplasmic ancestor gene-pools of musa acuminata colla and musa balb... 8002613 - The pcsa gene is identical to dind in escherichia coli. |
Publication Detail:
|
Type: Journal Article Date: 2011-11-23 |
Journal Detail:
|
Title: Standards in genomic sciences Volume: 5 ISSN: 1944-3277 ISO Abbreviation: Stand Genomic Sci Publication Date: 2011 Nov |
Date Detail:
|
Created Date: 2011-12-19 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 101530505 Medline TA: Stand Genomic Sci Country: United States |
Other Details:
|
Languages: eng Pagination: 203-10 Citation Subset: - |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, ...
Next Document: Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for...