Code for community-wide metabolic modelling, calculation of metabolite exchange scores (MES) and statistical tests

This repository contains the Python and R scripts needed to reproduce the analyses and graphs of the manuscript "Disease-specific loss of microbial cross-feeding interactions in the human gut". Additionally, this repository contains the Metagenome Assembled Genomes (MAGs) reconstructed. You can find here: * 24,369 high-quality MAGs (>90% completeness and <0.05% contamination). (all_HQ_bins_fasta.tar.gz) * 955 species-level MAGs (i.e. clustered at 95% ANI), used to build genome-scale metabolic models (nucleotide and aminoacid - spp_level_representative_MAGs.zip). This repository also contains the metabolic exchanges obtained from the community-wide modelling analysis (MICOM). Version 1.2.2 - When compared to v1.x, this version features: * Updated README with detailed steps of the analysis workflow. * Added scripts to produce new figures * Removed obsolete scripts

Related Organizations

Monash University
Australia
Institute for Systems Biology
United States
Hudson Institute of Medical Research
Australia

Keywords

metagenome-wide modeling, gut microbiome

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