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Genome Enrichment of Rare, Unknown Species from Complicated Microbiome by Nanopore Selective Sequencing

Yuhong Sun, Xiang Li, Qing Yang, Bixi Zhao, Ziqi Wu, Yu Xia
doi: https://doi.org/10.1101/2022.02.13.480078
Yuhong Sun
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Xiang Li
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
bState Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
cGuangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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Qing Yang
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Bixi Zhao
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Ziqi Wu
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Yu Xia
aSchool of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
bState Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
cGuangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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  • For correspondence: xiay@sustech.edu.cn
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Abstract

Rare species are vital members of a microbial community, but retrieving their genomes is difficult due to their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real-time, which provides an opportunity for enriching rare species. However, there is still a gap in RU-based enriching of rare and unknown species in environmental samples whose community composition is unclear, and many species lack corresponding reference in public databases. Here we present metaRUpore to overcome this challenge. We applied metaRUpore to a thermophilic anaerobic digester (TAD) community, it successfully redirected the sequencing throughput from high-abundance populations to rare species while facilitating the recovery of 41 high-quality metagenome-assembled genomes (MAGs) at low sequencing effort. The simplicity and robustness of the approach make it accessible for labs with moderate computational resources and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/sustc-xylab/metaRUpore.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 14, 2022.
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Genome Enrichment of Rare, Unknown Species from Complicated Microbiome by Nanopore Selective Sequencing
Yuhong Sun, Xiang Li, Qing Yang, Bixi Zhao, Ziqi Wu, Yu Xia
bioRxiv 2022.02.13.480078; doi: https://doi.org/10.1101/2022.02.13.480078
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Genome Enrichment of Rare, Unknown Species from Complicated Microbiome by Nanopore Selective Sequencing
Yuhong Sun, Xiang Li, Qing Yang, Bixi Zhao, Ziqi Wu, Yu Xia
bioRxiv 2022.02.13.480078; doi: https://doi.org/10.1101/2022.02.13.480078

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