Code and data for paper "Biotic resistance predictably shifts microbial invasion regimes" (https://www.nature.com/articles/s41467-025-59285-1)

./rawdata_experiment/ contains code and data files to reproduce all figures about experimental results (including predictions). Run figs_experiment.ipynb for plotting the figures. Data files for each figure are listed below.

• Fig.1c - SL_comp_cfu.xlsx
• Fig.1d - CM_comp_cfu.xlsx
• Fig.2c,d - SL_inv_OD.xlsx
• Fig.2e - CM_inv_luc.xlsx
• Fig.3b - SL_comp_cfu.xlsx (i, ii, iii), SL_inv_OD.xlsx (iii)
• Fig.3c - CM_comp_cfu.xlsx (i, ii, iii), CM_inv_luc.xlsx (iii)
• Sup Fig.1a - SL_pH.xlsx
• Sup Fig.1b,c - SL_growth_diffpH.csv (the growth curve, with a "Sample Layout" section within the file), SL_growth_diffpH_inipH.csv (the initial pH of the media)
• Sup Fig.2b - CM_comm_stability.xlsx
• Sup Fig.2c - CM_pH.xlsx
• Sup Fig.2d - CM_OD.csv
• Sup Fig.3 - SL_comp_cfu.xlsx
• Sup Fig.4 - CM_comp_cfu.xlsx
• Sup Fig.5 - SL_mig_CFU_timeseries_40mM.xlsx
• Sup Fig.6 - SL_inv_OD.xlsx
• Sup Fig.7 - CM_inv_luc.xlsx
• Sup Fig.8 - SL_comp_cfu.xlsx
• Sup Fig.9 - CM_comp_cfu.xlsx

Note: for sequencing and the simulated results as below, the raw data are available only in Figshare due to size limitations.

./raw_16S_sequencing/ contains raw Illumina sequencing files and the bash script for generating the read count table in ./rawdata_experiment/.

./rawdata_simulations/ contains code and data files to reproduce all figures about simulation results. Run figs_simulations.ipynb for plotting the figures. Processed data are available in pickle format in ./cr/ for Consumer-resource models and ./lv/ for Lotka-Volterra models. The raw simulation data are not necessary for reproducing the figures and are not provided due to their large size, but could be locally generated by running first main_simulations.py then analysis.py. See ./rawdata_simulations/readme_simulations.md for details.

• Fig. 4
• Sup Fig.10-19