Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA

ABSTRACT 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) sp...

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Autores principales:	Nora Grahl, Emily L. Dolben, Laura M. Filkins, Alex W. Crocker, Sven D. Willger, Hilary G. Morrison, Mitchell L. Sogin, Alix Ashare, Alex H. Gifford, Nicholas J. Jacobs, Joseph D. Schwartzman, Deborah A. Hogan
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	NanoString bacteria clinical microbiology cystic fibrosis fungi microbial communities Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e00226b7180942a295dba54c63ab9bf1
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spelling	oai:doaj.org-article:e00226b7180942a295dba54c63ab9bf12021-11-15T15:25:50ZProfiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA10.1128/mSphere.00292-182379-5042https://doaj.org/article/e00226b7180942a295dba54c63ab9bf12018-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00292-18https://doaj.org/toc/2379-5042ABSTRACT 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. IMPORTANCE Here 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.Nora GrahlEmily L. DolbenLaura M. FilkinsAlex W. CrockerSven D. WillgerHilary G. MorrisonMitchell L. SoginAlix AshareAlex H. GiffordNicholas J. JacobsJoseph D. SchwartzmanDeborah A. HoganAmerican Society for MicrobiologyarticleNanoStringbacteriaclinical microbiologycystic fibrosisfungimicrobial communitiesMicrobiologyQR1-502ENmSphere, Vol 3, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	NanoString bacteria clinical microbiology cystic fibrosis fungi microbial communities Microbiology QR1-502
spellingShingle	NanoString bacteria clinical microbiology cystic fibrosis fungi microbial communities Microbiology QR1-502 Nora Grahl Emily L. Dolben Laura M. Filkins Alex W. Crocker Sven D. Willger Hilary G. Morrison Mitchell L. Sogin Alix Ashare Alex H. Gifford Nicholas J. Jacobs Joseph D. Schwartzman Deborah A. Hogan Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
description	ABSTRACT 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. IMPORTANCE Here 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.
format	article
author	Nora Grahl Emily L. Dolben Laura M. Filkins Alex W. Crocker Sven D. Willger Hilary G. Morrison Mitchell L. Sogin Alix Ashare Alex H. Gifford Nicholas J. Jacobs Joseph D. Schwartzman Deborah A. Hogan
author_facet	Nora Grahl Emily L. Dolben Laura M. Filkins Alex W. Crocker Sven D. Willger Hilary G. Morrison Mitchell L. Sogin Alix Ashare Alex H. Gifford Nicholas J. Jacobs Joseph D. Schwartzman Deborah A. Hogan
author_sort	Nora Grahl
title	Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
title_short	Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
title_full	Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
title_fullStr	Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
title_full_unstemmed	Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA
title_sort	profiling of bacterial and fungal microbial communities in cystic fibrosis sputum using rna
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/e00226b7180942a295dba54c63ab9bf1
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Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA

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