Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron

Here, we present a technique to profile global gene expression of individual Bacteroides thetaiotaomicron cells. We describe steps for transcriptome stabilization and FACS-based collection and lysis of single Bacteroides cells.

We then detail procedures for reverse transcription, sensitive depletion of ribosomal sequences, and cDNA library generation. This experimental pipeline has potential to uncover cell-to-cell variability in predominant bacterial members of the healthy human gut microbiota.