Visualization of metabolic interaction networks in microbial communities using VisANT 5.0
Granger, Brian R.
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Citation (published version)Brian R Granger, Yi-Chien Chang, Yan Wang, Charles DeLisi, Daniel Segre, Zhenjun Hu. 2016. "Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0." PLOS COMPUTATIONAL BIOLOGY, Volume 12, Issue 4, pp. ? - ? (13). https://doi.org/10.1371/journal.pcbi.1004875
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.
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