Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanismsContains post sequence QC and post taxonomic and functional profiling "Source Data" used to generate tables and figures in Wallet et. al., "Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms" [1]. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA834801. Abstract: Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association at species and genus level, followed by network analysis to identify polymicrobial clusters, and functional profiling based on microbial genes and pathways. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters...This collection is openly accessible.Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms is published on Neuroscience AI.