論文 - 詳細
| RRC ID | 60605 |
|---|---|
| 著者 | Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. |
| タイトル | Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. |
| ジャーナル | Microbiome |
| Abstract |
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. |
| 巻・号 | 7(1) |
| ページ | 119 |
| 公開日 | 2019-8-27 |
| DOI | 10.1186/s40168-019-0737-z |
| PII | 10.1186/s40168-019-0737-z |
| PMID | 31455406 |
| PMC | PMC6712665 |
| MeSH | Bacteria / genetics Bacteria / isolation & purification Bacteriophages / genetics* Feces / microbiology* Gastrointestinal Microbiome* Gastrointestinal Tract / microbiology* Genome, Bacterial Humans Interspersed Repetitive Sequences / genetics Japan Metagenome / genetics* Plasmids / genetics* |
| IF | 11.607 |
| 引用数 | 1 |
| リソース情報 | |
| 一般微生物 | JCM10707 JCM12253 JCM16519 |