Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity

Single cell RNA sequencing is a technology
that provides the capability
of analyzing the transcriptome of a single cell from a population.
So far, single cell RNA sequencing has been focused mostly on human
cells due to the larger starting amount of RNA template for subsequent
amplification. One of the major challenges of applying single cell
RNA sequencing to microbial cells is to amplify the femtograms of
the RNA template to obtain sufficient material for downstream sequencing
with minimal contamination. To achieve this goal, efforts have been
focused on multiround RNA amplification, but would introduce additional
contamination and bias. In this work, we for the first time coupled
a microfluidic platform with multiple displacement amplification technology
to perform single cell whole transcriptome amplification and sequencing
of Porphyromonas somerae, a microbe
of interest in endometrial cancer, as a proof-of-concept demonstration
of using single cell RNA sequencing tool to unveil gene expression
heterogeneity in single microbial cells. Our results show that the
bacterial single-cell gene expression regulation is distinct across
different cells, supporting widespread heterogeneity.