Replication Data for: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease

*** DESCRIPTION *** Input data for replication of paper titled: \"Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease\". *** CONTENT *** - ApolloAgora2panSpecies: Folder with AGORA2 + APOLLO pan species gut microbe reconstructions. - luo_2024_replicated_PD_mets.xlsx: List of metabolites for which a replicated association with Parkinson's disease (PD) diagnosis was found by Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z) - metaboliteChemicalAnnotation.xlsx: Chemical annotations of PD-associated metabolites that mapped onto the blood compartment of WBM version 1.04c. Chemical annotations were taken from Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z). - metadata.xlsx: File with sample and patient metadata information. This file was taken and adapted from Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x) - mWBM_SET1-mWBM_SET5: Folder with microbiome personalised WBMs (version 1.04c). - PD_associatedTaxa_subsetPresentSpeciesMARS.xlsx: List of microbial species for which an association with PD diagnosis was found by Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x). - resultFlux: Folder with FBA flux solutions from the generated microbiome personalised WBMs. - resultMARS: Folder with gut microbiome mapping results after metagenomic mapping on the AGORA2+APOLLO pan species resource.