Skip to content

Detection of growth- and metabolism-altering interactions within a defined microbiota

Notifications You must be signed in to change notification settings

gregmedlock/asf_interactions

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

91 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

asf_interactions

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.

About

Detection of growth- and metabolism-altering interactions within a defined microbiota

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published