PDF(Pubmed)
Abstract：
A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.
摘要：
已经从人类肠道微生物组中鉴定出大量的微生物基因组,但是对低丰度物种在个体层面的作用的理解仍然具有挑战性，主要是由于大多数研究中使用的测序深度相对较浅。为了提高基因组组装性能，HiSeq-PacBio混合动力车,超深层宏基因组测序方法用于重建12个粪便样本的宏基因组组装基因组(MAG).这种方法将第三代测序与超深度第二代测序相结合，以提高肠道微生物组中低丰度亚群的测序覆盖率。我们的研究共产生了44兆碱基规模的支架，实现四个完整的单支架(环化，无间隙）MAG（CMAG）是其物种的第一个圆形基因组。此外，在所有样品中组装了475个高质量的MAG。其中,234个MAG目前未培养，包括在任何公共基因组数据库中未发现的24个MAG。此外,在每个个体中，287和77个MAG被分类为低丰度（0.1-1％）和超低丰度（<0.1％）的肠道物种，分别。我们的结果还揭示了MAG谱中的个体特异性基因组特征，包括微生物基因组的生长速率,选择性压力,和染色体可移动遗传元件的频率。最后,从宏基因组数据中识别出数千个染色体外移动遗传元件，包括5097个噬菌体和79个新的质粒基因组。总的来说,我们的策略代表了在个体水平上对人类肠道微生物组进行全面基因组和功能表征的重要一步.
