A site-independent approach towards functional genomics of polymicrobial interactions and uncharacterized gene function in Gram-positive bacteria

The overarching goals of our research are to understand how bacteria interact with their environment, to discover the function of uncharacterized bacterial genes ("dark matter" of the genome), and to build better biological resources that enable these studies.

We use genetic, biochemical, and computational tools to understand the molecular underpinnings of bacterial biofilms and interbacterial competition using Gram-positive bacteria such as Enterococcus and Streptococcus.  We leverage collections of clinical isolates from various body sites to ask fundamental questions about bacterial biofilms and gene function using diverse strain backgrounds.

Our work has important implications for the ecology of commensal microbiomes, treatment of biofilm-associated and polymicrobial infections, and biofilm-associated antibiotic resistance. 

1) Bacterial biofilm formation & stress response.  Biofilms are surface-associated (or aggregated) communities of microbes surrounded by a matrix.  Biofilm formation is a developmental process in which cells find and attach to a surface, build the extracellular matrix, and eventually disperse from the biofilms.  Critically, biofilm-associated cells are phenotypically distinct from their free-floating planktonic counterparts, making the study of biofilm-specific gene expression and response to stress conditions or antibiotic treatment inherently important in understanding how biofilms form during infection, how they contribute to antibiotic treatment failure, and how they impact the environment in general.

2) Interbacterial interactions & competition.  Bacteria are constantly interacting and competing with surrounding microbes for space and nutrients.  To do so, bacteria use numerous tools, including production of small protein toxins, metabolic changes, protein secretion systems, conjugative plasmids and DNA transfer systems, phage/prophage, and more.  We are particularly interested in the type 7 secretion systems (T7SS) found in Firmicutes.  In E. faecalis OG1RF, expression of the T7SS is regulated by phage and antibiotics, and delivery of T7SS effectors into neighboring bacteria results in a reduction in viability.  We are interested in characterizing the functional diversity of enterococcal T7SS effectors and understanding how T7SS-mediated competition influences community and microbiome dynamics. 

3) Functions of uncharacterized genes (the "dark matter" of bacterial genomes).  25-50% of gene products in the best-studied bacterial organisms are still annotated as uncharacterized or having an unknown function.  The actual percentage of these "dark matter" genes is probably much higher, given that only a small fraction of genes or gene products in a given bacterium have been studied and validated in that organism.  However, uncharacterized bacterial genes are frequently differentially expressed in conditions relevant to health and disease, and mutations in uncharacterized genes often have phenotypes in genetic screens.  We are interested in discovering fundamental gene function of "dark matter" genes using Enterococcus faecalis and other Gram-positive bacteria in order to understand how these genes contribute to health, infections, and general bacterial physiology.

4) Development of arrayed mutant/strain collections. Genetic tools such as collections of clinical isolates or arrayed mutant libraries facilitate rigor, reproducibility, and accessibility to scientific resources.  We maintain the arrayed, sequence E. faecalis OG1RF Tn library developed by Dr. Gary Dunny's lab and created the Functional Genomics Resource Center at the U Minnesota Genomics Center ( to facilitate use of these resources.  We are interested in expanding our collections and creating arrayed transposon mutant libraries in various understudied Gram-positive pathogens.