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Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Fig 3

Metabolic exchange in a microbial ecosystem.

Visualization of metabolic exchange between many organisms in a system is achieved through VisANT's multi-organism layout. The six organisms shown here are microbes selected because of their roles and abundance in the human gut. Metabolic flux was determined through a COMETS simulation involving all six microbes in a minimal D-glucose media. Each model is represented by a metanode, and in the center of the models are nutrients in the media that interact with the models. Nodes are color coded by their syntrophic influence, gray being nutrients involved in a potential syntrophy, red being nutrients which the microbes may be competing over, blue being nutrients which are produced by more than one organism, but consumed by none, and dark gray being nutrients which only have one model interacting with them. The network is simplified by hiding metabolite nodes that are not transported in/out by any model at this time point (normally displayed in white color), as well as metabolites not useful for biological interpretation of interactions, including biomass subcomponents (Protein_biosynthesis_e0, RNA_transcription_e0, and DNA_replication_e0) and highly connected ubiquitous metabolites (H2O_e0, H+_e0, Orthophosphate_e0). Minor manual rearrangement was conducted for the expanded network to improve clarity. Five of the six model metanodes are collapsed for clarity, but H. pylori is shown expanded, displaying the environmental exchange reactions. Nutrients of interest, Oxygen, D-Glucose, D-Galactose, (S)-Lactate, and Formate, have been labeled. Part of the L-Proline intracellular pathway has been expanded to exemplify VisANT’s capabilities.

Fig 3

doi: https://doi.org/10.1371/journal.pcbi.1004875.g003