sMETASeq: Combined Profiling of Microbiota and Host Small RNAs

Robin Mjelle; Kristin Roseth Aass; Wenche Sjursen; Eva Hofsli; Pål Sætrom

doi:10.1016/j.isci.2020.101131

sMETASeq: Combined Profiling of Microbiota and Host Small RNAs

iScience. 2020 May 22;23(5):101131. doi: 10.1016/j.isci.2020.101131. Epub 2020 May 4.

Authors

Robin Mjelle¹, Kristin Roseth Aass², Wenche Sjursen³, Eva Hofsli⁴, Pål Sætrom⁵

Affiliations

¹ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway. Electronic address: robin.mjelle@ntnu.no.
² Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Centre of Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7030, Norway.
³ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Department of Medical Genetics, St. Olavs Hospital, Trondheim 7030, Norway.
⁴ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; The Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, Trondheim 7030, Norway.
⁵ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Department of Computer and Information Science, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway.

Abstract

Understanding microbial communities' roles in human health and disease requires methods that accurately characterize the microbial composition and their activity and effects within human biological samples. We present sMETASeq (small RNA Metagenomics by Sequencing), a novel method that uses sequencing of small RNAs to jointly measure host small RNA expression and create metagenomic profiles and detect small bacterial RNAs. We evaluated the performance of sMETASeq on a mock bacterial community and demonstrated its use on different human samples, including colon cancer, oral leukoplakia, cervix cancer, and a panel of human biofluids. In all datasets, the detected microbes reflected the biology of the different sample types.

Keywords: Bioinformatics; Genomics; Microbiology.