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

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