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Nat Commun. 2018 Dec 17;9(1):5353. doi: 10.1038/s41467-018-07675-z.

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

Author information

1
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
2
Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.
3
School of Computer Science and Technology, Shandong University of Technology, Zibo, Shandong, China.
4
Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA.
5
Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
6
Argonne National Laboratory, Lemont, IL, 60439, USA.
7
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA. taopan@uchicago.edu.
8
Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA. taopan@uchicago.edu.
9
Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA. meren@uchicago.edu.
10
Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. meren@uchicago.edu.
11
Marine Biological Laboratory, Woods Hole, MA, 02543, USA. meren@uchicago.edu.

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.

PMID:
30559359
PMCID:
PMC6297222
DOI:
10.1038/s41467-018-07675-z
[Indexed for MEDLINE]
Free PMC Article

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