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 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.
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Granger
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.|Center for Advanced Genomic Technology, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Yi-Chien
authors.initials: YC
authors.lastname: Chang
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.|Center for Advanced Genomic Technology, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.|Center for Advanced Genomic Technology, Boston University, Boston, Massachusetts, United States of America.|Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: DeLisi
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America.|Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.|Department of Biology, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Daniel
authors.initials: D
authors.lastname: Segrè
authors.affiliation: Center for Advanced Genomic Technology, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Zhenjun
authors.initials: Z
authors.lastname: Hu
mesh_terms: D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D006801:Humans; D053858:Metabolic Networks and Pathways; D059013:Microbial Consortia / Q000502:physiology*; D064307:Microbiota / Q000502:physiology; D008954:Models, Biological; D012984:Software; D049490:Systems Biology