Enterosignatures define common bacterial guilds in the human gut microbiome (data)

Additional data related to the manuscript Enterosignatures define common bacterial guilds in the human gut microbiome. The deposit contains the following files: GMR_dataset.zip - data and results related to enterosignature computation in the GMR dataset: raw data, enterosignature composition, metabolic potentials of the associated metagenomic species GMR_dataset ├── NMF_results # results of NMF decomposition, from k = 2 signatures to 10, 5 being the optimal number │ ├── 10_H.tsv │ ├── .... │ ├── 9_W.tsv │ └── README.txt ├── age_metadata.tsv # age of individuals in the GMR dataset ├── drama_MGS_gtdbtk_taxonomy.tsv # taxonomy of the MGS ├── drama_genus_level_abundance.tsv # genus-level abundance table used for NMF └── metabo_data # Metabolic potential of the MGS associated to the enterosignatures ├── cazymes_by_genome.tsv # cazymes ├── gene_numbers.tsv # number of genes ├── kegg_metabolic_processes_by_genome.tsv # Kegg annotations ├── level1_onto_metabolites.tsv # Metacyc classes of metabolites, highest level ├── level2_onto_metabolites.tsv # Metacyc classes of metabolites, second level ├── metabolic_producers_full_community.tsv # predicted producers of metabolites, all genomes considered ├── metabolic_producers_withinES.tsv # predicted producers of metabolites, within an ES └── westerndiet.sbml # nutrients considered for metabolic modelling BMIS_dataset.zip - data and results related to enterosignature computation in the BMIS dataset BMIS_dataset ├── bmis_es_composition.tsv # ES assignments of BMIS samples (ES computed on the GMR dataset) ├── bmis_es_et_assignments.tsv # ES and enterotype assignments of BMIS samples └── bmis_genus-level_abundance.tsv # genus-level abundance matrix used for ES abundance computation NonWestern_dataset.zip - data and results related to enterosignature computation in the non-western dataset NonWestern_dataset ├── nonwestern_es_composition.tsv # ES assignments of Non-western samples (ES computed on the GMR dataset) └── nonwestern_genus_abundance_normalised.tsv # genus-level abundance matrix used for ES abundance computation The data is also available in the following repository: https://gitlab.inria.fr/cfrioux/enterosignature-paper/. See also https://enterosignatures.quadram.ac.uk/.