This repository includes data and analyses found in Auchtung, T.A. Lerma, A.I., Schuchart, K., and Auchtung, J.M. "Comparing effects of antibiotics in experimental models of human gastrointestinal microbial communities". The folders are uploaded as a zipped directory to maintain file structure.Overall metadata describing samples in the experiment can be found in the excel file: Auchtung et al overall Metdata.Much of the data processing is split by models, with data primarily collected from MBRA found in the "MBRA Analysis Files" directory and from human microbiota associated mice in the directory "MICE_Analysis_Files".There are two excel files that span across the two models that are in the home directory.There are two GraphPad prism files that include the data analysis present in many of the figures.The R_Code_and_Input_Files contains both the R code used for analysis as well as the input files used to create figures.Finally, the R output used for figures in the R figure files directory.