Experimental Approaches for Studying the Biofilm Matrix

Biofilms are bacterial aggregates encased in an extracellular matrix. The extracellular matrix is composed of extracellular DNA (eDNA), proteins, and exopolysaccharides. Biofilms protect bacteria from antibiotics and the host immune system, leading to chronic infections, and the biofilm matrix is a key aspect of these properties. Thus, there is great interest in studying the structure, regulation, and functions of biofilms and biofilm matrices. In this chapter, we discuss different methods that are used to study biofilm matrices, including examples of how they have been used, as well as some of their limitations. One method that we discuss is the use of stains which include small molecule dyes, such as Congo red, and lectins to stain biofilm matrix components such as eDNA and exopolysaccharides. We additionally discuss the use of confocal microscopy in conjunction with stains to visualize live biofilms and specific components of biofilm matrices. Lastly, we discuss nuclear magnetic resonance (NMR)—both solution and solid-state—as a unique tool to study biofilm matrices. In general, the examples that we draw on focus on biofilms formed by either Pseudomonas aeruginosa or Escherichia coli, although they are broadly applicable to studying the matrices of other biofilm-forming organisms as well.