Characterizing microbial community viability with RNA-based high-throughput sequencing

Characterization of microbial viability is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active (viable) community members. 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the viable components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for viability assessment in synthetic and environmentally-sourced microbial communities. We sequenced 192 samples using 16S-RNA-seq. Our results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent relative viability in realistic communities.