Visualization of metabolic interaction networks in microbial communities using VisANT 5.0
Abstract
Here, 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.
- Authors:
-
- Boston Univ., Boston, MA (United States). Bioinformatics Program
- Boston Univ., Boston, MA (United States). Bioinformatics Program; Center for Advanced Genomic Technology
- Boston Univ., Boston, MA (United States). Center for Advanced Genomic Technology; Dept. of Biomedical Engineering
- Boston Univ., Boston, MA (United States). Bioinformatics Program; Dept. of Biomedical Engineering; Dept. of Biology
- Boston Univ., Boston, MA (United States). Center for Advanced Genomic Technology
- Publication Date:
- Research Org.:
- Boston Univ., MA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1262270
- Grant/Contract Number:
- SC0004962
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Computational Biology (Online)
- Additional Journal Information:
- Journal Name: PLoS Computational Biology (Online); Journal Volume: 12; Journal Issue: 4; Journal ID: ISSN 1553-7358
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; biology markup language; flux balance analysis; systems biology; user-interface; models; reconstruction; platform; project; gene; metabolic networks; metabolics; network analysis; special interactions; enzyme metabolism; enzymes; consortia; microbial ecosystems
Citation Formats
Granger, Brian R., Chang, Yi -Chien, Wang, Yan, DeLisi, Charles, Segre, Daniel, and Hu, Zhenjun. Visualization of metabolic interaction networks in microbial communities using VisANT 5.0. United States: N. p., 2016.
Web. doi:10.1371/journal.pcbi.1004875.
Granger, Brian R., Chang, Yi -Chien, Wang, Yan, DeLisi, Charles, Segre, Daniel, & Hu, Zhenjun. Visualization of metabolic interaction networks in microbial communities using VisANT 5.0. United States. https://doi.org/10.1371/journal.pcbi.1004875
Granger, Brian R., Chang, Yi -Chien, Wang, Yan, DeLisi, Charles, Segre, Daniel, and Hu, Zhenjun. Fri .
"Visualization of metabolic interaction networks in microbial communities using VisANT 5.0". United States. https://doi.org/10.1371/journal.pcbi.1004875. https://www.osti.gov/servlets/purl/1262270.
@article{osti_1262270,
title = {Visualization of metabolic interaction networks in microbial communities using VisANT 5.0},
author = {Granger, Brian R. and Chang, Yi -Chien and Wang, Yan and DeLisi, Charles and Segre, Daniel and Hu, Zhenjun},
abstractNote = {Here, 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.},
doi = {10.1371/journal.pcbi.1004875},
journal = {PLoS Computational Biology (Online)},
number = 4,
volume = 12,
place = {United States},
year = {Fri Apr 15 00:00:00 EDT 2016},
month = {Fri Apr 15 00:00:00 EDT 2016}
}
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Towards zoomable multidimensional maps of the cell
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Competitive and cooperative metabolic interactions in bacterial communities
journal, September 2011
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Systems biology markup language: Level 2 and beyond
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SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks
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FAME, the Flux Analysis and Modeling Environment
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The Earth Microbiome project: successes and aspirations
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Spatially-resolved metabolic cooperativity within dense bacterial colonies
journal, March 2015
- Cole, John A.; Kohler, Lars; Hedhli, Jamila
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The COMBREX Project: Design, Methodology, and Initial Results
journal, August 2013
- Anton, Brian P.; Chang, Yi-Chien; Brown, Peter
- PLoS Biology, Vol. 11, Issue 8
Environments that Induce Synthetic Microbial Ecosystems
journal, November 2010
- Klitgord, Niels; Segrè, Daniel
- PLoS Computational Biology, Vol. 6, Issue 11
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
journal, February 2012
- Zomorrodi, Ali R.; Maranas, Costas D.
- PLoS Computational Biology, Vol. 8, Issue 2
Clostridium difficile Is an Autotrophic Bacterial Pathogen
journal, April 2013
- Köpke, Michael; Straub, Melanie; Dürre, Peter
- PLoS ONE, Vol. 8, Issue 4
Modeling cancer metabolism on a genome scale
journal, June 2015
- Yizhak, Keren; Chaneton, Barbara; Gottlieb, Eyal
- Molecular Systems Biology, Vol. 11, Issue 6
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
journal, January 2013
- Heinken, Almut; Sahoo, Swagatika; Fleming, Ronan M. T.
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