Additional file 11 of Four functional profiles for fibre and mucin metabolism in the human gut microbiome

Additional file 11. Dataset count matrices, Profile decomposition and metadata. The input data needed for the analysis are provided. • Metadata.xlsx: excel file containing the metadata of all the datasets used in the analysis. Field definition: – Sample_ID : internal ID. – ProjectID : study accession number. – SRA : SRA sample accession ID. – Patient_ID : internal patient ID. – Nationality, sex, age, BMI : patient nationality, sex, age and BMI. – Diagnosis : internal diagnosis code. N = healthy, CD = Crohn’s disease, UC = Ulcerative colitis, Control = Control sample, ObCIII = class 3 obesity, ObCII = class 2 obesity, ObCI= class 1 obesity, OW = overweight (but not obese), UW = underweight, PD = Parkinson disease, HC = healthy control, Diab = diabetis, ankylosing_spondylitis = ankylosing spondylitis. – Dysbiosis_index : dysbiosis index computed from HMP2 samples (see material and methods), Is_dysbiotic = above or under dysbiotic threshold (see material and methods). – Study : internal study ID. – reference : doi of the related publication. – alias : internal alias of the sample (HMP2 dataset only). – enterotype : sample enterotypes (metacardis dataset only). – Statin : statin intake (metacardis dataset only). – Bristol : Bristol score (metacardis dataset only). – Diet : diet taken by the patient (control or Mediterranean diet, med diet dataset only). – Timepoint : baseline, 4_weeks, 8_weeks (med_diet dataset only). • W.xlsx: weight matrix for the different datasets. • X_AFT.xlsx: AFT count matrix for the different datasets. The header indicates the AFT names as in Table 2. • X_mgs.xlsx: MGS count matrix at the genus level (train dataset only). • X_pg.xlsx: Prevalent genomes count matrix for the different datasets. The first sheet indicates the NCBI taxonomy ID and the name of the 203 prevalent genomes included in the study. • Genome_list.xlsx: list of the 203 genomes included in the study. • H.xlsx: matrices $$H^{(AFT)}, H^{(PG)}, H^{(mgs)}, H^{(AFT, mtx)}, H^{(PG, nmf)}$$ H ( A F T ) , H ( P G ) , H ( m g s ) , H ( A F T , m t x ) , H ( P G , n m f )  and  $$H^{(mgs, nmf)}$$ H ( m g s , n m f ) . • W_NMF_taxonomy.xlsx: weight matrix for the different datasets, for taxonomy-only NMF. • List_of_Reactions.xlsx: List of reactions as indicated in Fig. 1 and Table 2, with complete aggregated biochemical reaction, and reactant names. • F.xlsx: matrix of metabolic constraints used during NMF.