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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 (MAGs) 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 genomes of <jats:italic>Collinsella<\/jats:italic> and <jats:italic>Prevotella<\/jats:italic>, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that <jats:italic>Ruminococcus bromii<\/jats:italic> was statistically significantly (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.002) 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 (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05) related genes, such as <jats:italic>speF<\/jats:italic> 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.<\/jats:p>","DOI":"10.1038\/s41598-024-69742-4","type":"journal-article","created":{"date-parts":[[2024,8,14]],"date-time":"2024-08-14T16:02:36Z","timestamp":1723651356000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Metagenome-assembled microbial genomes from Parkinson\u2019s disease fecal samples"],"prefix":"10.1038","volume":"14","author":[{"given":"Ilhan Cem","family":"Duru","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Lecomte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T\u00e2nia Keiko","family":"Shishido","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pia","family":"Laine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joni","family":"Suppula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars","family":"Paulin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filip","family":"Scheperjans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro A. 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