BACKGROUND Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity. RESULTS Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids. CONCLUSIONS Overall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.

中文翻译：

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对人类肠道染色体外移动遗传元件的长篇宏基因组探索。


背景技术由于其高度复杂性和多样性，阐明人类肠道中染色体外移动遗传元件（eMGE）（例如质粒和噬菌体）的生态和生物学特性仍然具有挑战性。结果在这里，我们展示了从 PacBio 长读长宏基因组数据中有效识别 eMGE 作为完整的圆形或线性重叠群。对 12 个粪便样本进行 PacBio 长读段从头组装，生成 82 个 eMGE 重叠群（2.5~666.7-kb），分为 71 个质粒和 11 个噬菌体，其中包括 58 个新型质粒和 6 个噬菌体，以及 5 个不同 crAssphages 的完整基因组直接重复。在来自五个国家的 413 个肠道宏基因组的数据集中，许多已识别的质粒非常丰富且普遍。我们的质粒数据中肠道质粒的比例是公共数据库中的两倍多。在这个宏基因组数据集中，质粒与细菌染色体的数量平均为三比一。宿主预测表明，无论微生物丰度如何，拟杆菌相关质粒占主导地位。分析发现了几种富含质粒的功能，例如无机离子运输，而抗生素抗性基因主要存在于低丰度变形菌相关质粒中。结论 总体而言，长读长宏基因组学为揭示人类肠道 eMGE（尤其是质粒）的完整结构提供了一种有效的方法。