Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing

Sun，Yuhong1; Cheng，Zhanwen1; Li，Xiang1,2,3; Yang，Qing1; Zhao，Bixi1; Wu，Ziqi1; Xia，Yu2,3,4

2023-04-01

10.1101/gr.277266.122

Genome research   影响因子和分区

1088-9051

1549-5469

Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of 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. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.

SCI

英语

NI论文

第一

National Key Research and Development Program of China[2022YFE0103200] ; National Natural Science Foundation of China["42007216","42277103"]

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity

WOS:000999622400006

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT

MOLECULAR BIOLOGY & GENETICS

2-s2.0-85159738024

Scopus

1.School of Environmental Science and Engineering,College of Engineering,Southern University of Science and Technology,Shenzhen,518055,China
2.State 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
3.Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control,School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China
4.School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China;

Sun，Yuhong,Cheng，Zhanwen,Li，Xiang,et al. Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing[J]. Genome research,2023,33(4):612-621.

Sun，Yuhong.,Cheng，Zhanwen.,Li，Xiang.,Yang，Qing.,Zhao，Bixi.,...&Xia，Yu.(2023).Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.Genome research,33(4),612-621.

Sun，Yuhong,et al."Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing".Genome research 33.4(2023):612-621.