Profiling of bacterial and fungal microbial communities in cystic fibrosis sputum using RNA

• Published in: bioRxiv
• Main Authors: Grahl, Nora, Dolben, Emily L, Filkins, Laura M, Crocker, Alex W, Willger, Sven D, Morrison, Hilary G, Sogin, Mitchell L, Ashare, Alix, Gifford, Alex H, Jacobs, Nicholas J, Schwartzman, Joseph D, Hogan, Deborah A
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 01.06.2018
• Subjects: Abundance; Bacteria; Cystic fibrosis; DNA probes; Fungi; Genera; Microbiomes; rRNA 16S; Sputum
• DOI: 10.1101/336230

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 forty two bacterial and fungal genera or species common in cystic fibrosis (CF) sputum, and demonstrated taxon-specificity of these probes as well as a linear response over more than three 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. 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.