> For the complete documentation index, see [llms.txt](https://docs.kbase.us/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.kbase.us/workflows/metabolic-models/metabolic-flux-models.md). # Constructing and Analyzing Metabolic Flux Models of Microbial Communities 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. ### **Abstract** 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. ### **Narratives** * Single-Species Model Reconstruction and Analysis: * Mixed-Bag Model Reconstruction and Analysis: * Mixed-Bag Model Reconstruction and Analysis (VERSION 2): * Multi-Species Model Reconstruction and Analysis: * Species Interaction Analysis: **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](http://link.springer.com/protocol/10.1007%2F8623_2016_215). *Hydrocarbon and Lipid Microbiology Protocols*, 10.1007/8623\_2016\_215. Visit our [Publications page](https://www.kbase.us/research/) for more articles that describe research done using KBase. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.kbase.us/workflows/metabolic-models/metabolic-flux-models.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.