Open resource metagenomics: a model for sharing metagenomic libraries.
Open resource metagenomics: a model for sharing metagenomic libraries.
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DOI：
10.4056/sigs.1974654
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发表时间：
2011-11-30
影响因子：
--
通讯作者：
Charles TC
中科院分区：
文献类型：
--
作者：
Neufeld JD;Engel K;Cheng J;Moreno-Hagelsieb G;Rose DR;Charles TC
环境DNA的基于序列和基于活性的利用提供了对培养和未培养微生物的基因组内容的前所未有的访问。尽管研究人员将微生物菌株存款在培养物收藏中，并将DNA序列存入数据库，但基于活性的宏基因组研究通常只公布从特定筛选中检索到的命中序列。物理宏基因组文库，概念上类似于整个序列数据集，通常不是直接获得的出版后感兴趣的各方。为了促进宏基因组文库的不受限制的分布，我们建议采用开放资源宏基因组学，符合开放获取出版的趋势，并且类似于传统微生物学和微生物遗传学的支柱的培养物和质粒菌株收集。开放资源宏基因组学的概念包括制备物理DNA文库，优选地在促进在多种宿主生物体中筛选的通用载体中，以及合并克隆，使得含有完整文库的单个等分试样可以根据要求容易地分配。每个文库的相关元数据和序列数据的数据库沉积为研究人员提供了信息，以选择最合适的文库用于进一步的研究项目。作为一个起点，我们已经建立了加拿大MetaMicroBiome图书馆（CM 2BL）。CM 2BL是一个可公开访问的粘粒库集合，其中包含从加拿大各地收集的土壤环境DNA，跨越多个生物群落。构建文库使得克隆的DNA可以容易地转移到Gateway®顺应性载体，从而促进在存在可用质粒载体的几乎任何替代微生物宿主中的功能筛选。我们将这些图书馆置于公共领域，将根据要求不受限制地分发给学术研究界和工业界的成员。这篇文章邀请科学界采用这种开放资源宏基因组学的理念，将功能宏基因组学的实用性扩展到最初的出版物之外，从而避免了每个新研究项目都需要从头开始。
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 (CM2BL). The CM2BL 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.
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影响因子：
12.3
作者：
Raes J;Korbel JO;Lercher MJ;von Mering C;Bork P
通讯作者：
Bork P
影响因子：
4.4
作者：
Wang, CX;Meek, DJ;Charles, TC
通讯作者：
Charles, TC
影响因子：
2.9
作者：
Kim, Jeffrey H.;Feng, Zhiyang;Bauer, John D.;Kallifidas, Dimitris;Calle, Paula Y.;Brady, Sean F.
通讯作者：
Brady, Sean F.
影响因子：
5.1
作者：
Hao Y;Winans SC;Glick BR;Charles TC
通讯作者：
Charles TC
影响因子：
3
作者：
Meyer, F.;Paarmann, D.;Edwards, R. A.
通讯作者：
Edwards, R. A.