🔬 EMBOMicroCom: Metabolite and species dynamics in microbial communities 🧬
- Predict metabolic interactions within microbial communities
- Explore the effect of media composition on the predicted metabolite exchanges
- Interpret predicted metabolic interactions and evaluate against experimental data
- Case study: Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow
- Intro to FBA: What is flux balance analysis?
- SMETANA: Metabolic dependencies drive species co-occurrence in diverse microbial communities
- CarveMe: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
models/bacteria.xml: Manually refined Lactococcus lactis genome scale metabolic modelmodels/yeast.xml: Manually refined Saccharomyces cerevisiae genome scale metabolic modelmedia.tsv: Media composition file used for simulation under differing environmentsbigg_classes.tsv: BiGG metabolite ID dictionary and metadataplot_interactions.R: Rscript for generating alluvial diagrams based on SMETANA output
- Start by cloning this repo
- Inspect metabolic models and media file
- Simulate community interactions between bacteria and yeast
- Explore effect of interactions as a function of media composition
- Generate metabolic models and predict interactions using your own genomes (BONUS)
- SymbNET: From Metagenomics to Metabolic Interactions tutorial
- EMBOMicroCom tutorials: Daniel Machado's complementary exercises
- metaGEM_paper: metaGEM paper results
- metaGEM_unseenbio: metaGEM analysis of unseen bio at-home-test WGS sequencing data
- Cooccurrence paper: Supplement repo to cooccurrence paper
- CarveMe paper: Supplement repo to CarveMe paper
- Kefir paper: Supplement repo to kefir paper
- EMBL GEMs: Collection of RefSeq-based GEMs
- metaGEM: Reconstruction and simulation of genome scale metabolic models directly from metagenomes
- DesignMC: Design microbial communities for production of specific target compounds using GEMs
- HiOrCo: Compute higher order cooccurence using abundance across samples
- Reframed: Metabolic modeling package
- Francisco Zorrilla, MRC Toxicology Unit - University of Cambridge
- Kiran R. Patil, MRC Toxicology Unit - University of Cambridge