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Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

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VisANT visualization of metabolic cross-feeding between two bacteria, using the new “Symbiotic Layout” functionality.

This specific system is a previously evolved, obligate syntrophic consortium between a genetically modified E. coli strain which requires an external supply of methionine, and a S. enterica strain that cannot use the only carbon source available in the environment (lactose). The system was simulated with COMETS (Computation of Microbial Ecosystems in Time and Space), and represented in VisANT. For this case study we used a single spatial point (i.e. a 1 by 1 grid in COMETS), thus loading one grid point or the entire simulated COMETS grid are equivalent. Models are represented as expanded metanodes, exchange reactions are shown as nodes with (X,Y) graphs representing the flux through them throughout the simulated growth experiment, with an arrow denoting the current time step. Extracellular metabolite nodes are color coded based on the type of interaction they mediate: (i) Blue if it is secreted by both organisms; (ii) Red if it is consumed by both; (iii) Light gray if one model produces it and the other consumes it, and (iv) Dark gray if the metabolite is only associated with one model. E. coli can be seen here taking up lactose, and secreting acetate as a by-product. S. enterica, in turn, is able to grow using the acetate, and secretes methionine, which allows E. coli to continue to grow. Users can trace through the network by double-clicking a node to reveal connected nodes. This was used to trace lactose through the E. coli network, and to display some of the intracellular reactions adjacent to the exchange fluxes in S. enterica. In order to make the differences in fluxes more apparent for the reactions that mediate interactions between the two species, all the corresponding fluxes were mapped logarithmically onto the edge weights, using the "Rescale Selected Edges Logarithmically” function (see User Manual–Rescale Selected Edges Logarithmically at Page 10, S1 Text).

Fig 2

doi: https://doi.org/10.1371/journal.pcbi.1004875.g002