human lung metagenome targeted loci cystic fibrosis

We report an approach to detect diverse bacterial and fungal taxa incomplex samples by direct analysis of community RNA in one stepusing NanoString probe sets. We designed rRNA-targeting probe sets todetect forty two bacterial and fungal genera or species common incystic fibrosis (CF) sputum, and demonstrated taxon-specificity ofthese probes as well as a linear response over more than three logsof input RNA. Culture-based analyses correlated qualitatively withrelative abundance data on bacterial and fungal taxa obtained byNanoString and the analysis of serial samples demonstrated the useof this method simultaneously detect bacteria and fungi and todetect microbes at low abundance without an amplification step. Therelative abundances of bacterial taxa detected by analysis of RNAcorrelated strongly with the relative abundances of the same taxa asmeasured by sequencing of the 16S rRNA gene amplified from communityDNA from the same sample. This method may complement other methodsdesigned to understand dynamics microbial communities, may provideinformation on bacteria and fungi in the same sample with a singleassay, and, with further development, may provide quick andeasily-interpreted diagnostic information on diverse bacteria and fungiat the genus or species level. PI Deborah Hogan