Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Schwartz, Michael H.; Wang, Haipeng; Pan, Jessica N.; Clark, Wesley C.; Cui, Steven; Eckwahl, Matthew J.; Pan, David W.; Parisien, Marc; Owens, Sarah M.; Cheng, Brian L.; Martinez, Kristina; Xu, Jinbo; Chang, Eugene B.; Pan, Tao; Eren, A. Murat

doi:10.1038/s41467-018-07675-z

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Journal Article · Mon Dec 17 00:00:00 EST 2018 · Nature Communications

DOI:https://doi.org/10.1038/s41467-018-07675-z· OSTI ID:1569276

Schwartz, Michael H. ^[1]; ^[2]; Pan, Jessica N. ^[3]; Clark, Wesley C. ^[3]; Cui, Steven ^[4]; Eckwahl, Matthew J. ^[3]; Pan, David W. ^[3]; ^[3]; Owens, Sarah M. ^[5]; Cheng, Brian L. ^[6]; Martinez, Kristina ^[4]; Xu, Jinbo ^[7]; Chang, Eugene B. ^[4]; Pan, Tao ^[1]; ^[8]

Univ. of Chicago, Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology and Committee on Microbiology
Univ. of Chicago, Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Shandong Univ. of Technology, Zibo, Shandong (China). School of Computer Science and Technology; Toyota Technological Inst. at Chicago, Chicago, IL (United States)
Univ. of Chicago, Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology
Univ. of Chicago, Chicago, IL (United States). Dept. of Medicine
Univ. of Chicago, Chicago, IL (United States). Dept. of Medicine; Argonne National Lab. (ANL), Argonne, IL (United States)
Univ. of Chicago, Chicago, IL (United States). Committee on Microbiology
Toyota Technological Inst. at Chicago, Chicago, IL (United States)
Univ. of Chicago, Chicago, IL (United States). Committee on Microbiology and Dept. of Medicine; Marine Biological Lab., Woods Hole, MA (United States)

Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat-and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: China Scholarship Council; National Institutes of Health (NIH); National Natural Science Foundation of China (NNSFC); National Natural Science Foundation of Shandong Province; University of Chicago, Chicago, IL (United States); W.M. Keck Foundation, Los Angeles,CA (United States)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1569276

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 9; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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