Please run the following to get started:

git clone https://github.com/rhowardstone/ubiome.git
cd ubiome
chmod +x run.sh
./run.sh > logs.txt

The majority of the results of the paper (doi: 10.3389/fmicb.2025.1632210) will be reproduced, with figures appearing in 04_Analysis/Figs/, and data tables in 04_Analysis/data.