Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.
Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.
复制标题
使用 RNA 对囊性纤维化痰中的细菌和真菌微生物群落进行分析。
DOI：
10.1128/msphere.00292-18
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发表时间：
2018
期刊：
影响因子：
4.8
通讯作者：
Hogan,DeborahA
中科院分区：
文献类型：
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作者：
Grahl,Nora;Dolben,EmilyL;Filkins,LauraM;Crocker,AlexW;Willger,SvenD;Morrison,HilaryG;Sogin,MitchellL;Ashare,Alix;Gifford,AlexH;Jacobs,NicholasJ;Schwartzman,JosephD;Hogan,DeborahA
在这里，我们报告了一种方法，通过使用NanoString探针集直接分析群落RNA，一步检测复杂样品中的多种细菌和真菌分类群。我们设计了rrna靶向探针组，用于检测囊性纤维化（CF）痰液中常见的42种细菌和真菌属或种，并证明了这些探针的分类群特异性，以及对超过3 log输入RNA的线性响应。基于培养的分析与NanoString获得的细菌和真菌分类群的相对丰度数据定性相关，并且对系列样品的分析表明，该方法可以同时检测细菌和真菌，并且可以在没有扩增步骤的情况下检测低丰度的微生物。在属水平上，通过RNA分析检测到的细菌类群的相对丰度与从同一样品的群落DNA中扩增的16S rRNA基因V4V5区测序检测到的细菌类群的相对丰度相关。我们认为，该方法可以补充其他旨在了解动态微生物群落的方法，可以通过一次分析提供同一样品中细菌和真菌的信息，并且随着进一步发展，可以在属或种水平上提供快速且容易解释的不同细菌和真菌的诊断信息。在这里，我们展示了在微生物群落中使用基于rna的特定分类群分析，包括细菌和真菌。这种多重方法可以作为一种有用的手段来识别具有特定分类群组合的样本，并获得关于特定种群如何随时间和空间变化或对扰动的响应的信息。一种快速测量细菌和真菌种群的方法可能有助于研究宿主对微生物群落变化的反应。
Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes, as well as a linear response over more than 3 logs of input RNA. Culture-based analyses correlated qualitatively with relative abundance data on bacterial and fungal taxa obtained by NanoString, and the analysis of serial samples demonstrated the use of this method to simultaneously detect bacteria and fungi and to detect microbes at low abundance without an amplification step. Compared at the genus level, the relative abundances of bacterial taxa detected by analysis of RNA correlated with the relative abundances of the same taxa as measured by sequencing of the V4V5 region of the 16S rRNA gene amplified from community DNA from the same sample. We propose that this method may complement other methods designed to understand dynamic microbial communities, may provide information on bacteria and fungi in the same sample with a single assay, and with further development, may provide quick and easily interpreted diagnostic information on diverse bacteria and fungi at the genus or species level.IMPORTANCEHere we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host response to changes in microbial communities.