Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces

BMC Research Notes

Research Note

Tomoya Baba¹  Yuh Shiwa²  JangKeun Kim³  Christopher E. Mason⁴  Haruo Suzuki⁵  Maria A. Sierra⁶ 

[1] Advanced Genomics Center, National Institute of Genetics, Mishima, Japan;Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan;Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan;NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan;Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA;The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA;Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA;The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA;The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA;Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan;Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan;Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA;

关键词: rRNA depletion;    Virus detection;    Environmental metatranscriptome analysis;    Virome;    Library preparation;   

DOI  :  10.1186/s13104-023-06417-9

 received in 2022-12-17, accepted in 2023-06-23,  发布年份 2023

来源: Springer

【 摘 要 】

ObjectiveMetatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity using a mock community and a melamine-coated table surface RNA with levels below those required (< 5 ng) with a library preparation kit (NEBNext Ultra II Directional RNA Library Prep Kit).ResultsGood-quality RNA libraries were obtained from 0.1 ng of mock community and table surface RNA by changing the adapter concentration and number of PCR cycles. Differences in the target species of the rRNA depletion method affected the community composition and sensitivity of virus detection. The percentage of viral occupancy in two replicates was 0.259 and 0.290% in both human and bacterial rRNA-depleted samples, a 3.4 and 3.8-fold increase compared with that for only bacterial rRNA-depleted samples. Comparison of SARS-CoV-2 spiked-in human rRNA and bacterial rRNA-depleted samples suggested that more SARS-CoV-2 reads were detected in bacterial rRNA-depleted samples. We demonstrated that metatranscriptome analysis of RNA viromes is possible from RNA isolated from an indoor surface (representing a built-environment surface) using a standard library preparation kit.

【 授权许可】

CC BY   
© The Author(s) 2023

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