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

Michael H. Schwartz, Haipeng Wang, Jessica N. Pan, Wesley C. Clark, Steven Cui, Matthew J. Eckwahl, David W. Pan, Marc Parisien, Sarah M. Owens, Brian L. Cheng, Kristina Martinez, Jinbo Xu, Eugene B. Chang, Tao Pan () and A. Murat Eren ()
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Michael H. Schwartz: University of Chicago
Haipeng Wang: University of Chicago
Jessica N. Pan: University of Chicago
Wesley C. Clark: University of Chicago
Steven Cui: University of Chicago
Matthew J. Eckwahl: University of Chicago
David W. Pan: University of Chicago
Marc Parisien: University of Chicago
Sarah M. Owens: University of Chicago
Brian L. Cheng: University of Chicago
Kristina Martinez: University of Chicago
Jinbo Xu: Toyota Technological Institute at Chicago
Eugene B. Chang: University of Chicago
Tao Pan: University of Chicago
A. Murat Eren: University of Chicago

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract 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.

Date: 2018
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DOI: 10.1038/s41467-018-07675-z

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