NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

BMC Bioinformatics

Elhanan Borenstein³  Shiri Freilich¹  Anat Kreimer⁴  Rogan Carr²  Roie Levy² 

[1]Newe Ya’ar Research Center, Agricultural Research Organization, Ramat Yishay, 30095, Israel

[2]Department of Genome Sciences, University of Washington, Seattle 98195, WA, USA

[3]Santa Fe Institute, Santa Fe 87501, NM, USA

[4]Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco 94158, CA, USA

关键词: Reverse ecology;    Metabolic networks;    Systems biology;    Community assembly;    Microbial ecology;    Species interactions;   

Others  :  1232563
DOI  :  10.1186/s12859-015-0588-y

 received in 2015-01-12, accepted in 2015-04-22,  发布年份 2015

【 摘 要 】

Background

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.

Results

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.

Conclusions

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. webcite

【 授权许可】

   
2015 Levy et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 1.

Figure 2.

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