Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms

Abstract Parkinson’s disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, 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. Thirty-percent of species and pathways tested had altered abundances in PD, depicting a widespread dysbiosis. Network analysis showed PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. Metagenomic profile of PD indicates a disease permissive microbiome, 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. These data provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.