Application of RNA-seq and bioimaging methods to study microbe–microbe interactions and their effects on biofilm formation and gene expression

Abstract

Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. We describe two different experimental approaches to study microbe–microbe interactions in in vitro systems containing surface-associated microbial populations. One method is the application of RNA sequencing (RNA-seq) to determine the transcriptional changes in pathogenic bacteria in response to microbial interspecies interactions. The other method combines flow cell devices for bacterial cultivation and growth with high-resolution bioimaging to analyze the microscale structural organization of interacting microbial populations within mixed-species biofilms.