This git repository accompanies the paper "Metabolic mechanisms of interaction within a defined gut microbiota", available on bioRxiv here.
In this study, we profiled the growth and metabolism of 6 bacterial strains from the altered Schaedler flora (ASF), a group of bacteria used to standardize the mouse microbiota in breeding facilities. We grew each of the 6 strains in monoculture and co-culture, profiling growth interactions using probe-based qPCR and metabolic behavior using 1H-NMR spectroscopy-based metabolomics. We developed an applied a Constant Yield Expectation (ConYE, pronounced "Kanye") model, which we used in conjunction with genome scale metabolic network reconstructions to dissect metabolic cross-feeding.
This repository contains all data, models, and analyses associated with the study. We are currently uploading raw NMR spectra to MetaboLights (a MS/NMR metabolomics database) and prepping a Jupyter notebook to demonstrate loading/manipulating the processed data for "data mutualists" (less tastefully known as "data parasites") to re-use. Within our paper, we focus our genome-scale metabolic network analysis on a single strain, but we provide network reconstructions for 7 of the ASF strains here,constructed using the same methods.