RT Journal
A1 Sun, Yuhong
A1 Cheng, Zhanwen
A1 Li, Xiang
A1 Yang, Qing
A1 Zhao, Bixi
A1 Wu, 
Ziqi
A1 Xia, Yu
T1 Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
JF Genome Research 
JO Genome Research 
YR 2023 
FD April 01 
VO 33 
IS 4 
SP 612 
OP 621 
DO 10.1101/gr.277266.122 
UL http://genome.cshlp.org/content/33/4/612.abstract 
AB 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.