High-throughput screening alternative to crystal violet biofilm assay combining fluorescence quantification and imaging.

The crystal violet assay is widely used for biofilm quantitation despite its toxicity and variability. Here, we instead combine fluorescence labelling with the Cytation 5 multi-mode plate reader, to enable simultaneous acquisition of both quantitative and imaging biofilm data. This high-throughput method produces more robust data and provides information about morphology and spatial species organization within the biofilm.

Application of RNA-seq and Bioimaging Methods to Study Microbe-Microbe Interactions and Their Effects on Biofilm Formation and Gene Expression.

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.

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories.

Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.

Genome Sequence of Pseudomonas aeruginosa Strain DK1-NH57388A, a Stable Mucoid Cystic Fibrosis Isolate.

Pseudomonas aeruginosa is an important opportunistic pathogen associated with chronic pulmonary infections and mortality in cystic fibrosis (CF) patients. Here, we present the complete genome sequence of stable mucoid P. aeruginosa strain DK1-NH57388A, a CF isolate which has previously been used to establish chronic lung infections in an animal model.