NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.
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DOI：
10.1186/s12859-015-0588-y
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发表时间：
2015-05-17
影响因子：
3
通讯作者：
Borenstein E
中科院分区：
文献类型：
--
作者：
Levy R;Carr R;Kreimer A;Freilich S;Borenstein E
宿主-微生物和微生物-微生物相互作用通常由代谢物的复杂交换控制。这种相互作用在确定病原体和寄生物种影响其宿主的方式以及复杂微生物群落的组装方面发挥着关键作用。最近，一些研究已经证明了这种相互作用如何反映在相互作用物种的代谢网络的组织中，并引入了各种基于图论的方法来直接从网络拓扑结构预测宿主-微生物和微生物-微生物相互作用。利用这些方法，这些研究揭示了形成物种相互作用和群落组装的进化和生态过程，突出了这种反向生态学研究范式的潜力。NetCooperate是一个基于网络的工具和软件包，用于确定宿主-微生物和微生物-微生物合作潜力。它专门计算了两个先前开发和验证的物种相互作用的指标：生物合成支持评分，量化了宿主物种提供寄生或寄生物种营养需求的能力，以及代谢互补性指数，量化了一对微生物生物体的互补性。NetCooperate将一对代谢网络作为输入，并返回成对度量以及潜在互养代谢化合物的列表。生物合成支持评分和代谢互补性指数提供了对宿主-微生物和微生物-微生物代谢相互作用的深入了解。NetCooperate从代谢网络拓扑结构中确定这些相互作用指数，并可用于小规模或大规模分析。NetCooperate是以基于Web的工具和开源Python模块的形式提供的;两者都可以在http://elbo.gs.washington.edu/software_netcooperate.html上免费获得。
Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms’ niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.
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影响因子：
14.9
作者：
Kolenbrander PE
通讯作者：
Kolenbrander PE
影响因子：
64.5
作者：
Neph S;Stergachis AB;Reynolds A;Sandstrom R;Borenstein E;Stamatoyannopoulos JA
通讯作者：
Stamatoyannopoulos JA
影响因子：
--
作者：
Fadda, Abeer;Fierro, Ana Carolina;Marchal, Kathleen
通讯作者：
Marchal, Kathleen
影响因子：
5.8
作者：
Carr, Rogan;Borenstein, Elhanan
通讯作者：
Borenstein, Elhanan
影响因子：
4.3
作者：
Faust K;Sathirapongsasuti JF;Izard J;Segata N;Gevers D;Raes J;Huttenhower C
通讯作者：
Huttenhower C