Mapping human microbiome drug metabolism by gut bacteria and their genes

Data sets for analysis and visualization pipelines for screening the capacity of common gut bacteria to metabolize oral drugs.############################################################Analysis schemes are provided in AnalysisSchemes subfolder.Subfolders Input and Output contain tables and figure files to reproduce tables and figures from the corresponding study. See analysis schemes and the project code readme files for further details. ############################################################The project code is deposited on GitHub (https://github.com/mszimmermann/drug-bacteria-gene_mapping) and consists of four pipelines:1) Drug Screen AnalysisData are in Raw_DrugScreenAnalysis subfolder. Perform differential analysis and hierarchical clustering of the metabolism patterns of 271 oral drugs by 76 diverse human gut bacteria (and four pH controls).2) Drug Metabolism Products AnalysisData files are in Raw_DrugMetabolismProducts subfolder. Perform differential analysis of metabolites co-occuring with specific drugs measured by untargeted mass-spectrometry.3) Drug-metabolizing Gene Products AnalysisData files are in Raw_DrugMetabolizingGeneProducts subfolder. Perform protein identity analysis for the identified bacterial gene products.4) Gain-of-Function Screen AnalysisData files are in Raw_GainOfFunction subfolder. Reproduce other manuscript figures (including gain-of-function bacterial gene identification screen). ############################################################ This project is part of the work by Michael Zimmermann, Maria Zimmermann-Kogadeeva, Rebekka Wegmann and Andrew L. Goodman.