Supplemental Data

Supplimentary figures Supplementary_Dec 23 2023 Final .docx - Supplimentary figures from the paper. Metadata metadata.xlsx - Contains metadata for each mouse in the study. The sheets "MetagenomeData" and "MetaboliteData" denote metadata for the metagenomic and metabolite studies, respectively. Untargeted Metabolomics Data (Raw and intermediate data files) Metabolite_Data_OriginalScale.csv - Untargeted matbolomic data with values that were normalized in terms of raw area counts. Metabolite_Data_ScaledImp.csv - Untargeted metabolomics data after both additional normalization (each chemical in OriginalScale is rescaled to set the median equal to 1) and imputation (missing values are imputed with minimum). Samples were sent to Metabolon for untargeted metabolomics. All metadata for the mice is included in the first several rows of each spreadsheet or in the metadata file. Shotgun Metagenomics Data (Intermediate data files) TSS_OTU - Operational taxonomic unit (OTU) tables for the shotgun metagenomics after each sample has been normalized to 1 million reads (total sum scaling). Each table indicates a different kingdom of microbe (Archaea, fungi, etc). Each sheet in each Excel file indicates a different taxonomic level (Genus, etc). Rarefied_OTU - Operational taxonomic unit (OTU) tables for the shotgun metagenomics after each sample has been rarefied. Each table indicates a different kingdom of microbe (Archaea, fungi, etc). Each sheet in each Excel file indicates a different taxonomic level (Genus, etc). functionalAnalysis_allComparisons.xlsx - All results for the functional analyses at the gene, module, and pathway levels (the various subsheets of this Excel). Shotgun Metagenomics Data (Raw data files) Please see Sequence Read Archive (PRJNA1227428) for all raw (fastq level) metagenomic sequencing data. Manuscript Code Annotated code (R and python) used to perform the key analytic steps outlined in the associated paper (files start with "Code_").