Cell Chromatography: Biocompatible Chromatographic Separation and Interrogation of Microbial Cells

The isolation of pure, single colonies lies at the heart of experimental microbiology. However, a microbial colony typically contains around 1 million cells at all stages of the life cycle. Here, we describe a novel cell chromatography method that facilitates the capture, purification, and interrogation of microbial cell populations from both single and mixed cultures. The method described relies on, but is not limited to, differences in surface charge to separate bacterial strains. The method is fully biocompatible, leading to no significant loss of cell viability. The chromatographic capture of cells, combined with selective elution methods, facilitates a greater level of experimental control over the sample inputs required for downstream high-throughput and high-sensitivity analytical methods. The application of the method for interrogating the antibiotic resistance of bacterial strains and for the separation of bacteria from environmental samples is illustrated. IMPORTANCE This is the first report of a method for separating microbial cells using chromatography, with full retention of cell viability. Differences in the surface chemistry of microbial cells provides a means of attracting cells to immobilized microbeads. Some cells are attracted, and some are repelled. The differences in, for example, surface charge can be harnessed to capture, interrogate, and separate environmental samples, thus circumventing the need to use conventional bacterial plating methods. This method will greatly facilitate drug discovery and bioprospecting for novel microbial compounds.