Gianna Marschmann from Lawrence Berkeley National Laboratory presented at the KBase Microbial Community Modeling workshop. The title of the session was: DEBmicroTrait: Trait-based Microbial Community Modeling in KBase Overview.” Marschmann is a postdoc with Ulas Karaoz. Genome-informed trait-based modeling takes multidimensional data. Marschmann noted that they can reduce dimensionality and model traits. The parameter distributions can be used for ecosystem-scale modeling and global-scale modeling. Currently the ecosystem and global-scale modeling are in development. Marschmann and team developed two apps: microTrait and the Dynamic Energy budget Model (DEB). MicroTrait is a toolset for a trait-based representation of microbial genomes. The DEB and microTrait apps are both published in KBase and a public narrative is forthcoming. Ulas Karaoz went over the DEBmicroTrait Trait-based Microbial Community Modeling in KBase Narrative. Karaoz explained that they are using a dataset with 300 isolates involved in root growth and signaling. Karaoz and team used this data set to ask the question: How do we go from genomes to inferred fitness traits? For this, they focused on traits that fall into three categories: resource acquisition, resource use, and stress tolerance. The microTrait app takes genomes as input. The user defines the amount of variant in the guild. The output is a heat map of traits and genomes. Trait variance is also measured across genomes. Next, Marschmann demonstrated the Dynamic Energy Budget Model Simulations. The common root exudate metabolites from the plant species were used. Media type and chemical abundance are used to simulate guilds grow on all substrates in the trait matrix. There is also a mode to perform competitions. Percent uptake, for example, is generated. Substrate class preference is also calculated. Future developments of the DEB app will include expansion of parameters the app can accept. Marschmann also noted that they want to improve the chemical set system used for the app. I wonder how this would work for Delftia spp. in pairwise competitions…
