Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France.
Environ Microbiol. 2012 Feb;14(2):356-71. doi: 10.1111/j.1462-2920.2011.02559.x. Epub 2011 Sep 5.
Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.
设计环境 DNA 微阵列，使其能够用于调查自然界中存在的微生物的极端多样性，这是分子生态学领域的一个极具挑战性的任务。事实上，元基因组学的最新研究已经从各种生态系统中产生了大量的序列信息，并且由于下一代测序方法在定性和定量方面的改进，将会继续积累大量的序列数据。现在，可以利用这些数据，通过探索性探针设计策略来开发综合微阵列。这种策略可以预测遗传变异，从而能够检测环境样本中的已知和未知序列。在这篇综述中，我们详细介绍了目前可用于构建系统发育和功能 DNA 微阵列的探针设计策略，重点介绍了那些允许选择这种探索性探针的策略。此外，对复杂环境的探索需要特别注意探针的灵敏度和特异性标准。最后，这些创新的探针设计方法需要利用新的高密度微阵列格式。
