Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition
Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition
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DOI：
10.1371/journal.pone.0016900
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发表时间：
2011-02-24
期刊：
影响因子：
3.7
通讯作者：
Kelley, Scott T.
中科院分区：
文献类型：
--
作者：
Caporaso, J. Gregory;Knight, Rob;Kelley, Scott T.
系统发育分析已被广泛用于比较细菌群落，但迄今为止还不可能应用于病毒，因为缺乏类似于16S rRNA的单一标记基因。在这里，我们开发了一种用于匹配病毒序列的参考树方法，并将其应用于最大的病毒数据集。由此产生的技术Shotgun UniFrac用于比较宿主相关和非宿主相关的噬菌体群落（共130个宏基因组），并揭示了与细菌群落相似的深刻分裂。这种新的信息学方法补充了细菌群落的分析，并有望为病毒群落动态提供新的见解，例如在一系列系统中病毒对细菌群落的自上而下与自下而上的控制。
Phylogenetic profiling has been widely used for comparing bacterial communities, but has so far been impossible to apply to viruses because of the lack of a single marker gene analogous to 16S rRNA. Here we developed a reference tree approach for matching viral sequences and applied it to the largest viral datasets available. The resulting technique, Shotgun UniFrac, was used to compare host-associated and non-host-associated phage communities (130 total metagenomes), and revealed a profound split similar to that found with bacterial communities. This new informatics approach complements analysis of bacterial communities and promises to provide new insights into viral community dynamics, such as top-down versus bottom-up control of bacterial communities by viruses in a range of systems.