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 that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature, and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD. Zenodo contents: In this Zenodo archive we provide (1) post sequence QC and post taxonomic and functional profiling "Source Data" used to generate tables and figures in the manuscript and (2) "Supplementary Code" that contains the workflow and code used to perform bioinformatic processing of shotgun sequences and statistical analyses of microbial profiles and subject metadata. The code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA834801.

This work was funded by The U.S. Army Medical Research Materiel Command endorsed by the U.S. Army through the Parkinson's Research Program Investigator-Initiated Research Award under Award No. W81XWH1810508; NIH Training Grant T32NS095775; NIH/NIEHS 1R01ES032440-01A1 and Parkinson's Foundation PF-SF-JFA-830658; and Aligning Science Across Parkinson's [ASAP-020527] through the Michael J. Fox Foundation for Parkinson's Research. For the purpose of open access, at the time of publication, the authors have applied a CC BY public copyright license to all Author Accepted Manuscripts arising from this submission.