fermentation_products

This repository contains all data and code (analysis and illustrations) used in our study "Quantifying the daily fermentation product harvest from the human gut microbiota." Markus Arnoldini, Richa Sharma, Claudia Moresi, Griffin Chure, Julien Chabbey, Emma Slack, and Jonas Cremer

Jonas Cremer, Griffin Chure, and Markus Arnoldini

June 2025, Palo Alto

Directory Structure

This repository contains three major folders, each of which is described below.

analysis

This folder contains all the Python code used to analyze and illustrate variations in fermentation product excretion and harvest. Different Jupyter files contain different analysis parts. See the README file in the folder for additional information.

hplc_measurements

This folder contains the raw experimental data from our cultivation and HPLC measurements. The analysis code to extract growth rates, carbohydrate uptake, and excretion rates from measurements is also included. Plots summarizing all cultures are also available here. See the README file in the folder for additional information.

interactives

This folder contains all the Python and JavaScript code needed to generate the interactive figure. The website to show this figure is hosted on a separate branch (gh-phages) and accessible https://cremerlab.github.io/fermentation_products/ .

License

The software herein is licensed under an MIT license as follows: ``` Copyright 2024 The Authors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ```