Finding the needles in the metagenome haystack.
Finding the needles in the metagenome haystack.
复制标题
在元基因组干草堆中找到针。
DOI：
10.1007/s00248-006-9201-2
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发表时间：
2007-04
影响因子：
3.6
通讯作者：
van Veen, Johannes A.
中科院分区：
文献类型：
--
作者：
Kowalchuk, George A.;Speksnijder, Arjen G. C. L.;Zhang, Kun;Goodman, Robert M.;van Veen, Johannes A.
居住在地球不同环境中的微生物的集体基因组（宏基因组）中记载了这个星球上生命的历史。在过去的15年里，微生物生态学家开发和使用的新分子工具正在促进这些基因组的提取、克隆、筛选和测序。这种方法使微生物生态学家能够访问和研究全方位的微生物多样性，无论我们培养生物体的能力如何，并提供了前所未有的访问这些基因组编码的天然产物的广度。然而，在可预见的未来，仅仅收集序列，无论多么广泛，都无法完全覆盖微生物宏基因组的复杂世界。此外，尽管有可能从环境中的基因多样性海洋中钓出高度信息化和有用的基因，但这可能是一个非常繁琐和低效的过程。微生物生态学家必须聪明地在微生物多样性的巨大干草堆中追求生态相关的，有价值的和生态位定义的基因组信息。在这份报告中，我们试图描述的进展和前景，将有助于微生物生态学家收集更多的知识，从调查宏基因组。这些包括测序和克隆方法的技术进步，以及注释和比较序列分析的改进。然而，更重要的是，通过限制研究中的目标群体或提高筛选程序的重点或速度，将重点放在可能特别相关的宏基因组的各种子集上。最后，考虑到大型宏基因组项目所需的成本和基础设施，以及它们可以产生的几乎无穷无尽的数据量，整个研究界更广泛地使用宏基因组数据的趋势，加上专门用于宏基因组的生物信息学基础设施所需的投资无疑将进一步增加各种环境中宏基因组研究的价值。
In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth’s diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.
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