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) 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 t

SUBMITTER: Grahl N 

PROVIDER: S-EPMC6083091 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature