fodmapsandgutmicrobiome's Introduction

Dietary FODMAPs, Gut Microbiome and Health in Irritable Bowel Syndrome

Investigating the interplay between dietary FODMAPs, gut microbiome and health in irritable bowel syndrome (IBS) using data from multiple studies.

Reproducability

Step 0: Run install_packages.R to install required packages.
Step 1: Place the microbiome data for each study under the corresponding directory under (preprocessing/study_id/microbiome_data/). For some studies (s1, s3, s4), the raw microbiome data can be fetched using a corresponding fetch_data.sh script while for other studies (s2, s5, s6) they were directly requested from the article authors. See table below for the list of studies analyzed. See preprocessing/study_id/microbiome_data/format.txt for the expected format.
Step 2: Place the metadata for each study in preprocessing/study_id/metadata.csv with format specified at metadata_format.csv.
Step 3: Run run_all.sh and see the final figures under the results directory. Note that the preprocessing step was performed on cluster node with 64GB RAM and two Intel E5-2630 v3 2.4GHz CPU’s each having 8 cores and may take up to a day for a given study.

Requirements

QIIME 2 (version ≥ 2018.11)
PICRUSt (version 1.1.4)

Code Architecture

├─ fig/
   ├─ Fig1.png
   ├─ Fig5A.png
├─ integrated_analysis/
   ├─ generate_Fig2.R
   ├─ generate_Fig3.R
   ├─ ...
├─ lib/
   ├─ abundance_management.R
   ├─ classification.R
   ├─ ...
├─ preprocessing/
   ├─ s1/
   ├─ s2/
   ├─ ...
├─ install_packages.sh
├─ run_all.sh
├─ settings.txt

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