School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
ISME J. 2013 Mar;7(3):520-32. doi: 10.1038/ismej.2012.135. Epub 2012 Nov 22.
Bacteriophages are the most abundant biological life forms on Earth. However, relatively little is known regarding which bacteriophages infect and exploit which bacteria. A recent meta-analysis showed that empirically measured phage-bacteria infection networks are often significantly nested, on average, and not modular. A perfectly nested network is one in which phages can be ordered from specialist to generalist such that the host range of a given phage is a subset of the host range of the subsequent phage in the ordering. The same meta-analysis hypothesized that modularity, in which groups of phages specialize on distinct groups of hosts, should emerge at larger geographic and/or taxonomic scales. In this paper, we evaluate the largest known phage-bacteria interaction data set, representing the interaction of 215 phage types with 286 host types sampled from geographically separated sites in the Atlantic Ocean. We find that this interaction network is highly modular. In addition, some of the modules identified in this data set are nested or contain submodules, indicating the presence of multi-scale structure, as hypothesized in the earlier meta-analysis. We examine the role of geography in driving these patterns and find evidence that the host range of phages and the phage permissibility of bacteria is driven, in part, by geographic separation. We conclude by discussing approaches to disentangle the roles of ecology and evolution in driving complex patterns of interaction between phages and bacteria.
噬菌体是地球上最丰富的生物生命形式。然而，人们对于哪些噬菌体感染和利用哪些细菌知之甚少。最近的一项荟萃分析表明，经验测量的噬菌体-细菌感染网络通常具有显著的嵌套性，平均而言，而不是模块化的。一个完全嵌套的网络是指噬菌体可以从专家到通才进行排序，使得给定噬菌体的宿主范围是排序中后续噬菌体的宿主范围的子集。同样的荟萃分析假设，在更大的地理和/或分类学尺度上，模块性（其中噬菌体专门针对不同的宿主群体）应该出现。在本文中，我们评估了已知最大的噬菌体-细菌相互作用数据集，该数据集代表了从大西洋地理上分离的地点采样的 215 种噬菌体类型与 286 种宿主类型之间的相互作用。我们发现这个相互作用网络具有高度的模块化。此外，在这个数据集识别出的一些模块是嵌套的或包含子模块，这表明存在多尺度结构，正如早期的荟萃分析所假设的那样。我们研究了地理因素在驱动这些模式中的作用，并发现证据表明噬菌体的宿主范围和细菌的噬菌体允许性部分受到地理隔离的驱动。最后，我们讨论了分离生态和进化在驱动噬菌体和细菌之间复杂相互作用模式中的作用的方法。
