Metagenome-assembled microbial genomes from Parkinson’s disease fecal samples

The human gut microbiome composition has been linked to Parkinson’s disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAG) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different versions of Collinsella and Prevotella MAGs, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies. ### Competing Interest Statement FS: Grants from The Academy of Finland, The Hospital District of Helsinki and Uusimaa, OLVI-Foundation, Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse, The Wilhelm and Else Stockmann Foundation, The Emil Aaltonen Foundation, The Yrjo Jahnsson Foundation, The Sigrid Juselius Foundation, Renishaw. Honoraria: AbbVie, Axial Biotherapeutics, Orion, GE Healthcare, Merck, Teva, Bristol Myers Squibb, Sanofi, Biocodex, Lundbeck, and Biogen. Founder and CEO of NeuroInnovation Oy and NeuroBiome Ltd. Member of the advisory boards of Axial Biotherapeutics and MRM Health. Stock options from Axial Biotherapeutics. P.A.B.P., L.P., P.A., and F.S. have patents issued (FI127671B, US10139408B2, US11499971B2) and pending (US16/186,663, EP3149205) that are assigned to NeuroBiome Ltd. T.K.S. is funded by Novo Nordisk Foundation (NNF22OC0080109).