Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland.
Sci Rep. 2024 Aug 14;14(1):18906. doi: 10.1038/s41598-024-69742-4.
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 (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 Collinsella and Prevotella, 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.
人类肠道微生物群的组成与帕金森病（PD）有关。然而，我们对肠道微生物组在基因组水平上的了解仍然有限。在这里，我们对 136 个人类粪便微生物组（68 个 PD 样本和 68 个对照样本）进行了深度宏基因组测序和分箱，以构建宏基因组组装基因组（MAGs）。我们构建了 952 个非冗余的高质量 MAGs，并在 PD 和对照组之间进行了比较。在这些 MAGs 中，有 22 种不同的 Collinsella 和 Prevotella 基因组，表明这些属在人类肠道环境中具有高度的可变性。微多样性分析表明，与 PD 样本相比，Ruminococcus bromii 在控制样本中的菌株水平上具有统计学上显著（p<0.002）的更高多样性。此外，通过对所有基因进行聚类并在组间进行存在-缺失分析，我们鉴定了几个对照组特有的（p<0.05）相关基因，如 speF 和 Fe-S 氧化还原酶。我们还报告了 MAGs 的详细注释，包括直系同源基因簇（COG）、Cas 操纵子类型、抗病毒基因、噬菌体和次生代谢物生物合成基因簇，这可为未来的研究提供参考。
