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.

微生物活力的表征对于解析微生物群落的基础生物学特征至关重要，因为微生物组（microbiome）的功能由其具备生化活性（即存活）的群落成员所决定。基于16S rRNA转录本的扩增子测序（16S-RNA-seq）已被提出作为表征微生物组存活组分的可靠方法，但其应用效能尚未得到系统性评估。本研究针对人工合成与环境来源的微生物群落，开展了基于RNA的扩增子测序用于活力评估的基准测试工作。我们采用16S-RNA-seq对192份样本完成了测序，结果显示：尽管该方法可在相对简单的群落中半定量微生物活力，但在真实群落中仅能反映分类群依赖性的相对存活水平。