Code and material repository for "Quantifying the effects of diet on microbial communities across different gut contexts"

Analysis pipeline

1. biobakery workflows v3.0.0

   • KneadData v0.7.7

   • MetaPhlAn 3 v3.0

   • HUMAnN 3 v3.0.0

2. Basic statistics using various R package's listed throughout the manuscript and methods

3. Custom R scripts (src directory)

Directory Structure

• The /input directory contains the by-sample taxonomic profiles, metadata, and intermediate files generated for each study used in the analysis. This directory is organized by study and each study's directory contains /Initial and /Intermediate sub-directories.

• The src directory is the main source directory for all the custom scripts used for manuscript. The README in this directory describes the code and corresponding input and output files.

Accession numbers for raw data

• Mehta et al., 2018, Abu-Ali et al. 2018 (human adult); SRA PRJNA354235
• Lloyd-Price et al., 2019 (human adult); SRA PRJNA398089
• Smits et al., 2017 (human adult); SRA PRJNA392012, PRJNA392180
• Backhed et al., 2015 (human infant); EBI ERP005989
• Murphy et al., 2018 (human infant); SRA PRJNA345144
• Amato et al., 2015 (non-human primates); SRA SRP065516
• Faith et al., 2011 (mice); SRA SRP005394