Paper Info
Title
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
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 meta-graph 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.
Year
DOI
Venue
2016
10.1371/journal.pcbi.1004875
PLOS COMPUTATIONAL BIOLOGY
Field
DocType
Volume
Software tool,Biology,Biological network,Visualization,Microbiome,Systems biology,Interaction network,Bioinformatics,User interface,Flux balance analysis
Journal
12
Issue
ISSN
Citations 
4
1553-734X
1
PageRank 
References 
Authors
0.34
25
6
Name
Order
Citations
PageRank
Brian R Granger110.34
Yi-Chien Chang2734.44
Yan Wang3472.93
Charles Delisi448941.96
Daniel Segrè5534.83
Zhenjun Hu633924.50