Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut

Yoshihiko Suzuki, Suguru Nishijima, Yoshikazu Furuta, Jun Yoshimura, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Shinichi Morishita

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number119
JournalMicrobiome
Volume7
Issue number1
DOIs
Publication statusPublished - 2019 Aug 27

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Interspersed Repetitive Sequences
Metagenomics
Plasmids
Bacteriophages
Metagenome
Bacterial Chromosomes
Bacteroidetes
Proteobacteria
Terminal Repeat Sequences
Nucleic Acid Repetitive Sequences
Ion Transport
Microbial Drug Resistance

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Suzuki, Y., Nishijima, S., Furuta, Y., Yoshimura, J., Suda, W., Oshima, K., ... Morishita, S. (2019). Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome, 7(1), [119]. https://doi.org/10.1186/s40168-019-0737-z

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. / Suzuki, Yoshihiko; Nishijima, Suguru; Furuta, Yoshikazu; Yoshimura, Jun; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Morishita, Shinichi.

In: Microbiome, Vol. 7, No. 1, 119, 27.08.2019.

Research output: Contribution to journalArticle

Suzuki, Y, Nishijima, S, Furuta, Y, Yoshimura, J, Suda, W, Oshima, K, Hattori, M & Morishita, S 2019, 'Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut', Microbiome, vol. 7, no. 1, 119. https://doi.org/10.1186/s40168-019-0737-z
Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K et al. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome. 2019 Aug 27;7(1). 119. https://doi.org/10.1186/s40168-019-0737-z
Suzuki, Yoshihiko ; Nishijima, Suguru ; Furuta, Yoshikazu ; Yoshimura, Jun ; Suda, Wataru ; Oshima, Kenshiro ; Hattori, Masahira ; Morishita, Shinichi. / Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. In: Microbiome. 2019 ; Vol. 7, No. 1.
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