Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis
題目：利用高通量tRNA測序和調(diào)控分析描繪微生物組群特征
作者：
Michael H. Schwartz, Haipeng Wang, Jessica N. Pan, [...], Tao Pan & A. Murat Eren
通訊作者單位：
A. Murat Eren:
Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
Marine Biological Laboratory, Woods Hole, MA, 02543, USA
Tao Pan:
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
發(fā)表期刊及時間：
Nature Communications volume 9, Article number: 5353 (2018)
Published 17 December 2018
摘要：
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 mod- ifications within complex environmental microbiomes.
高通量測序的發(fā)展促進了人們對天然存在的微生物的多樣性和功能的卓越的認識呵燕；但是，現(xiàn)有的測序策略不足以揭示與蛋白質(zhì)翻譯動力學(xué)相關(guān)的微生物組群的生理狀態(tài)导梆。轉(zhuǎn)運RNA（tRNA）是蛋白質(zhì)合成工具的核心成分蜡坊，存在于所有活細胞當(dāng)中，在系統(tǒng)發(fā)育上很容易追溯，這些特征讓它們成為了獲得環(huán)境微生物生理學(xué)見解的理想靶點。這里丛肢，我們報道了一個直接的測序方法tRNA-seq，以及配套的軟件tRNA-seq-tools絮记，以復(fù)原微生物tRNA轉(zhuǎn)錄物的序列摔踱，豐度譜和轉(zhuǎn)錄后修飾虐先。我們使用tRNA-seq分析盲腸樣品怨愤，利用比較16S核糖體RNA基因擴增子的方式區(qū)分高脂肪和低脂肪喂養(yǎng)的小鼠，并揭示tRNA修飾中的分類和飲食依賴性變異蛹批。我們的研究結(jié)果提供了對復(fù)雜環(huán)境微生物組中tRNA基因表達和轉(zhuǎn)錄后修飾動態(tài)的分類特異性原位洞察撰洗。
圖表選析
Fig 3. Microbiome tRNA-seq workflow and taxonomy analysis. 圖3. 微生物組tRNA-seq工作流程和分類學(xué)分析
a Workflow of tRNA sequencing of gut microbiome samples fed with a high-fat (HF) or low- fat (LF) diet and de novo tRNA assignment. Conserved tRNA residues that were searched for in this work are shown in red.
b Dendrograms compare relationships between HF and LF samples that were inferred based on community profiles of tRNA transcripts, or 16S rRNA gene amplicons.
c Class-level taxonomy for averaged HF and LF samples based on tRNA-seq (top) and 16S rRNA gene amplicons (bottom). All bacterial classes at >1% level are shown in distinct colors, all other bacterial classes are grouped together and shown in purple.
d tRNAGly taxonomy for anticodons GCC, UCC, and CCC.
e tRNAGlu taxonomy for anticodons UUC and CUC. Among the other category for GCC/UCC/CCC and UUC, no class has an abundance of ≥1%; for CUC, other classes with an abundance of ≥1% include Alphaproteobacteria, Gemmatimonadetes, and Ignavibacteria. tRNAs decoding these two amino acids are the most abundant in our tRNA-seq results
a 用高脂肪飲食組（HF）或低脂肪飲食組（LF）的腸道微生物組樣品的tRNA測序以及tRNA重新匹配的工作流程篮愉。此工作中尋找到的保守tRNA殘基被標注為紅色。
b 系統(tǒng)樹圖差导，比較HF組和LF租兩個樣品的關(guān)系试躏，這些關(guān)系基于tRNA轉(zhuǎn)錄物或16S rRNA基因擴增子的群組特征推斷得到。
c 基于tRNA-seq（上圖）和16S rRNA基因擴增子（下圖）的平均HF和LF樣品的類級分類蔗喂。所有> 1％水平的細菌類別以不同的顏色顯示乡革，所有其他細菌類別組合在一起并以紫色顯示渐裸。
d 甘氨酸t(yī)RNA反密碼子GCC, UCC, 和 CCC 的分類.
e 谷氨酸t(yī)RNA反密碼子UUC和CUC的分類。在GCC / UCC / CCC和UUC的其他類別中犀被，沒有一個類別的豐度≥1％；對于CUC外冀，其他豐度≥1％的類別包括甲型變形菌（Alphaproteobacteria）寡键，芽單胞菌（Gemmatimonadetes）和Ignavibacteria（無中文名）。在我們的tRNA-seq結(jié)果中這兩種氨基酸的tRNA是最豐富的雪隧。
