The effects of dietary fat and fiber on the gut microbiome in the context of antibiotic-induced C. difficle infection

This repository includes all files produced through QIIME2 microbiome profiling of 16S rDNA sequencing FASTQ files along with visualizations and statistical analysis run in R. Analysis was optimized through a pipeline generated in Snakemake, associated files are contained in the workflow directory.

Directory contents are as follows:

• Arizona Experiments Combined (az_exp_combined): A re-run of lower QIIME2 16S rDNA sequencing analysis with the combination of cecal and stool sample data due to a lack of data points at sacrifice in the stool samples for the Arizona experiments (stool samples taken at sacrifice are filtered out, respectively).
• Cecum: 16S rDNA sequencing microbiome results, CD toxin, bile acid, short-chain fatty acid (SCFA), histologic scores, and hypoxia levels for mouse cecal contents at sacrifice from the Arizona experiments.
• Comparisons: A combination of baseline microbiome data from the Arizona experiments and new experiments conducted at CU Anschutz to make comparisons between studies (soon to be combined with data from this study).
• Figures: Compiled manuscript figures, plots taken from all directories.
• New Experiments (new_experiments): Preliminary results of follow-up mouse experiments currently being conducted at CU Anschutz.
• Stool: 16S rDNA sequencing microbiome results for mouse fecal stool samples taken throughout the experimental timeline to get a better picture of microbiome changes over time from the Arizona experiments.
• Workflow: Contains the pipeline built for the purpose of this data analysis in Snakemake (tutorial coming soon!).

Contact Information:

All code and subsequent outputs were generated by Madison Apgar, a graduate student in the Lozupone lab at the University of Colorado Anschutz Medical Campus.

• LinkedIn: Madi Apgar
• Email: madison.apgar@cuanschutz.edu