KBase has a suite of tools and data that support the reconstruction, prediction, and design of metabolic networks in individual microbes and microbial communities. A recent review article in Hydrocarbon and Lipid Microbiology Protocols discusses and compares approaches to modeling the growth and behavior of microbial communities, and shows how to perform the analyses in KBase. The analysis workflows described in the article are available as Narratives (linked below) that you can copy to your own KBase account and rerun, perhaps changing some of the parameters or adding your own datasets..
Here we provide a broad overview of current research in modeling the growth and behavior of microbial communities, while focusing primarily on metabolic flux modeling techniques, including the reconstruction of individual species models, reconstruction of mixed-bag models, and reconstruction of multi-species models. We describe how flux balance analysis may be applied with these various model types to explore the interactions of a microbial community with its environment, as well as the interactions of individual species with each other. We demonstrate all discussed model reconstruction and analysis approaches using the Department of Energy’s Systems Biology Knowledgebase (KBase), constructing and importing genome-scale metabolic models of Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii and subsequently combining them into a community model of the gut microbiome. We also use KBase to explore how these species interact with each other and with the gut environment, exploring the trade-offs in information provided by applying each metabolic flux modeling approach. Overall, we conclude that no single community modeling approach is better than the others, and often there is much to be gained by applying multiple approaches synergistically when exploring the ecology of a microbial community.
Single-Species Model Reconstruction and Analysis: https://narrative.kbase.us/narrative/ws.10779.obj.1
Mixed-Bag Model Reconstruction and Analysis: https://narrative.kbase.us/narrative/ws.10786.obj.1
Mixed-Bag Model Reconstruction and Analysis (VERSION 2): https://narrative.kbase.us/narrative/notebooks/ws.15122.obj.2
Multi-Species Model Reconstruction and Analysis: https://narrative.kbase.us/narrative/ws.10824.obj.1
Species Interaction Analysis: https://narrative.kbase.us/narrative/ws.10778.obj.1
Reference: Faria JP, Khazaei T, Edirisinghe J, Weisenhorn PB, Seaver S, Conrad N, Harris N, DeJongh M, Henry CS (2016) Constructing and Analyzing Metabolic Flux Models of Microbial Communities. Hydrocarbon and Lipid Microbiology Protocols, 10.1007/8623_2016_215.
Visit our Publications page for more articles that describe research done using KBase.