This repository houses all data and code (analysis and illustration) used in our study "Quantifying the daily fermentation product harvest from the human gut microbiota".
Jonas Cremer, Griffin Chure, Markus Arnoldini
This repository is broken down into three major folders with their content described in the following.
This directory contains all the Python code used to analyze and illustrate variations in fermentation product excretion and harvest. Different Jupyter files contain different analysis parts, named in order as they corresponding analysis appears in the manuscript. E.g. starting with the analysis and plotting of fermentation product secretion.
This directory contains the experimental data of our hplc measurements. Analysis code to extract from measurements growth rates and carbohydrate uptake and excretion rates are also included here.
This directory contains all the Python and JavaScript code needed to generate the interactive figures in this work. The interactive website is hosted on a second repository: https://github.com/cremerlab/microbiome-fermentation-products
The software herein is licensed under an MIT license as follows:
Copyright 2024 The Authors
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