Some considerations for analyzing biodiversity using integrative metagenomics and gene networks
Some considerations for analyzing biodiversity using integrative metagenomics and gene networks
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DOI：
10.1186/1745-6150-5-47
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发表时间：
2010-07-30
期刊：
影响因子：
5.5
通讯作者：
Bapteste, Eric
中科院分区：
文献类型：
--
作者：
Bittner, Lucie;Halary, Sebastien;Bapteste, Eric
背景：提高对生物多样性的了解将有利于保护生物学，加强生物修复研究，并可能带来新的医学治疗方法。然而，没有标准方法来估计和比较不同环境的多样性，或研究其过去和可能的未来演化。 假设的提出：我们认为，在生物多样性的识别和量化方面取得重大进展需要满足两个条件。首先，综合宏基因组研究——旨在同时检查（甚至更好地整合）多个标记的大规模测序所捕获的元素、功能和进化过程的观察结果——应该优先于DNA条形码项目和基于单个标记的宏基因组项目。其次，此类宏基因组数据应采用新颖的包容性网络方法进行研究，旨在对环境中存在的许多单位和许多过程进行推论。检验假设：我们通过比较两种寻求评估生物多样性的分子方法的理论基础得出了这些结论：宏基因组学（主要用于原核生物和原生生物）和DNA条形码（主要用于多细胞真核生物），并通过对由生物多样性引起的问题的务实考虑得出了这些结论。生物多样性研究中的“物种问题”。该假设的含义：进化基因网络降低了以有限的解释力产生生物多样性估计的风险，这些估计要么因 LGT 比率不均而产生偏差，要么由于 I 型和 II 型灰色区域引起的（实际）问题而难以解释。此外，这些网络可以轻松容纳额外的（元）转录组和（元）蛋白质组数据。 审稿人：本文由 Pr. 审阅。 William Martin、David Williams 博士（由 J Peter Gogarten 教授提名）和 James McInerney 博士（由 John Logsdon 教授提名）。
Background: Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.Presentation of the hypothesis: We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.Testing the hypothesis: We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.Implications of the hypothesis: Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta) transcriptomic and (meta) proteomic data.Reviewers: This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon).