Bacterial communities react to environmental stressors, the presence of oxygen in the gut, for example, by changing their transcriptional landscapes, and these responses underlie microbiome-related disorders such as inflammatory bowel disease (IBD), and colorectal cancer (CRC). Although RNAseq has been used to profile community function to obtain dynamic functional information not captured by metagenomic DNA sequencing alone, RNAseq is unable to capture real-time dynamics due to the varying stability of RNA, requires additional steps to remove ribosomal RNA, and isoften insensitive to short non-coding or modified RNA. We propose the development of Precision Run-On and SEQuencing (PRO-seq) as a promising method to capture transcriptional dynamics in cultured prokaryotes and in complex microbial communities, such as the human microbiome.