Using network analysis to explore co-occurrence patterns in soil microbial communities
Using network analysis to explore co-occurrence patterns in soil microbial communities
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DOI：
10.1038/ismej.2011.119
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发表时间：
2012-02-01
期刊：
影响因子：
11
通讯作者：
Fierer, Noah
中科院分区：
文献类型：
--
作者：
Barberan, Albert;Bates, Scott T.;Fierer, Noah
探索由高通量DNA测序技术产生的大型环境数据集需要新的分析方法，以超越对天然微生物群落组成和多样性的基本清单描述。为了研究微生物类群之间的潜在相互作用，网络分析的重要类群共现模式可能有助于破译复杂的微生物群落的结构跨越空间或时间梯度。在这里，我们计算了微生物分类群之间的关联，并将网络分析方法应用于16 S rRNA基因条形码焦磷酸测序数据集，该数据集包含来自广泛生态系统类型的151个土壤样本的>160 000个细菌和古细菌序列。我们描述了由此产生的网络的拓扑结构，并定义了基于丰度和占用（即，栖息地通才和栖息地专家）的操作分类单元类别。共现模式很容易揭示，包括一般的非随机协会，共同的生活史策略在广泛的分类水平和社区成员之间的意想不到的关系。总体而言，我们展示了探索类群间相关性的潜力，以获得对微生物群落结构和指导群落组装的生态规则的更全面的了解。The ISME Journal（2012）6，343-351; doi：10.1038/ismej.2011.119; 2011年9月8日在线发表
Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial communities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial communities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined operational taxonomic unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad taxonomic levels and unexpected relationships between community members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly. The ISME Journal (2012) 6, 343-351; doi: 10.1038/ismej.2011.119; published online 8 September 2011