Based on the original work done by Natasa Mortvanski for her Master project in 2023 (MSc Bioinformatics for Health Sciences 2021/2023)

Title of the publication: The Clinical Value of Alpha-diversity metrics to establish Dysbiosis in Microbiome Studies

This is a repository containing the R project with the following directories:

• 00_raw_data:

  Contains all raw data files used for the analysis. The data from choosen studies was downloaded from Qiita repository (https://qiita.ucsd.edu/). For each analysed study preparation file was downloaded (metadata table) as well as results of alpha diversity analysis in a form of tsv file.

  Following studies were used as source of samples of different pathological conditions that affect alpha diversity:

  1. Subset of the American Gut Project dataset -> dataset link
  2. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases -> 177 samples, dataset link
  3. Metaomics Reveals Microbiome Based Proteolysis as a Driver of Ulcerative Colitis Severity -> 96 samples, dataset link
  4. Guiding longitudinal sampling in inflammatory bowel diseases cohorts -> ...samples , dataset link
  5. Gut microbiome predictors of treatment response and recurrence in primary Clostridium difficile infection -> BioProject study accession: PRJNA342347
  6. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection -> 95 samples, dataset link
  7. Changes in Microbial Ecology after Fecal Microbiota Transplantation for recurrent C. difficile Infection Affected by Underlying Inflammatory Bowel Disease -> 95 samples, dataset link
  8. Hospital Clinic's CDI and donor data (only alpha diversity metrics files and metadata)

  For all of the studies above, following alpha metrics wese computed:

  • Shannon's entropy
  • Chao1 index
  • Menhinick's richness index
  • Margalef's richness index
  • Fisher's index
  • Simpson's index
  • Gini index
  • Strong's dominance index
  • Pielou's evenness
  • Faith's Phylogenetic Diversity

• 01_tidy_data:

  Contains processed tables with choosen metadata variables (columns) and all computed alpha metrics that are used in further analysis.

• 02_R_scripts:

  Contains all Rmd files for the analysis.

• 03_plots_and_tables:

  Contains plots and tables generated in the analysis.

• 04_reports:

  Contains HTML reports generated from Rmd files.

• 05_functions:

  Contains make_reports.R - this script defines function report that makes HTML reports out of Rmd scripts and stores them in 04_reports directory.

• run_all.r:

  Script that utilize the make_reports.R function and creates HTML reports for all Rmd files in the project.

• Supplementary material