PDF(Pubmed)
Abstract：
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.
摘要：
人类肠道微生物组组成与帕金森病(PD)有关。然而,在基因组水平上对肠道微生物群的了解仍然有限。在这里，我们进行了深度宏基因组测序和分级，以从136个人类粪便微生物组（68个PD样品和68个对照样品）构建宏基因组组装的基因组（MAG）。我们构建了952个非冗余高质量MAG，并在PD组和对照组之间进行了比较。在这些MAG中，Collinsella和Prevotella有22个不同的基因组,表明这些属在人类肠道环境中的高度变异性。微多样性分析表明,与PD样品相比,在对照样品中的菌株水平上,Brouminococus在统计学上显著(p<0.002)更多样化。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，我们确定了几个对照特异性（p<0.05）相关基因，如speF和Fe-S氧化还原酶。我们还报告了MAG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，预言,和次级代谢产物生物合成基因簇，为今后的研究提供参考。
