HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota

Chan Yeong Kim, Junyeong Ma, Insuk Lee

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.

Original languageEnglish
Article number6367
JournalNature communications
Issue number1
Publication statusPublished - 2022 Dec

Bibliographical note

Funding Information:
This research was supported by the National Research Foundation (NRF) & funded by the Korean government (MSIT) (No. 2018R1A5A2025079, 2019M3A9B6065192, and 2022M3A9F3016364 to I.L.) and supported in part by the Brain Korea 21 (BK21) FOUR Program to I.L. HiFi sequencing was provided by the SMRT Grant of MdxK, Macrogen, and PacBio to I.L.

Publisher Copyright:
© 2022, The Author(s).

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • General
  • Physics and Astronomy(all)


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