Abstract
The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT’s unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the “symbiotic layout” of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.
Highlights
Metabolism comprises a complex network of biochemical reactions that guarantee a supply of energy and building blocks to every living cell
Focused on the interaction network between bio-molecules in its first release [28], VisANT gradually expanded its scope into the fields of systems biology, systems pharmacology and translational science with the support of metagraph capability [29,30,31,34] and integrated knowledge of diseases, therapies and drugs [32]
While in the current work we describe in detail only analyses performed using COMETS output files, the capacity of VisANT to represent community-level networks from other sources (e.g. SBML files generated from Model SEED [42]) is detailed in the User Manual–Working with your own data, at Page 5 (S1 Text)
Summary
Metabolism comprises a complex network of biochemical reactions that guarantee a supply of energy and building blocks to every living cell. The new functions in VisANT 5.0 are built around three main data types: (i) The network models, which can be uploaded from SBML (Systems Biology Markup Language) files [39,40,41], from COMETS input files, or from a tab-delimited edge-lists that includes the specification of node type; (ii) The flux matrix, containing information on the rates (or fluxes) of different reactions in different organisms at different time points. While in the current work we describe in detail only analyses performed using COMETS output files, the capacity of VisANT to represent community-level networks from other sources (e.g. SBML files generated from Model SEED [42]) is detailed in the User Manual–Working with your own data, at Page 5 (S1 Text).
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