Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

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.系统发育谱（phylogenetic profiling）已被广泛应用于细菌群落的比较分析，但此前因缺乏类似16S核糖体RNA（16S rRNA）的单一标记基因，始终无法将其应用于病毒研究。本研究开发了一种用于匹配病毒序列的参考树方法，并将其应用于现有最大规模的病毒数据集。由此得到的Shotgun UniFrac技术被用于比较宿主关联与非宿主关联的噬菌体群落（共包含130个宏基因组样本），结果揭示出与细菌群落相似的显著群落分化模式。这一新型信息学方法可作为细菌群落分析的有效补充，有望为病毒群落动态研究提供全新见解，例如在多种生态系统中病毒对细菌群落的自上而下与自下而上调控机制。