In nature, bacteria are highly organized; whether in the soil, on the surface of a tooth, or in a chronic wound. In many environments, bacteria have been observed as small dense clusters of cells called aggregates, separated by micrometer distances. Although we still don’t understand why bacteria adopt these distinct physical distributions, we have shown that spatial organization is critical for virulence (Stacy et al. 2014). We are currently studying how bacterial cells spatially organize themselves at the micro-scale, using a variety of techniques. Using synthetic CF sputum (SCFM2) and wound like medias, we are able to observe the development of bacterial communities in these environments using high resolution microscopy and image analysis pipelines. Thus allowing us to resolve spatial organization at the individual aggregate level, in three-dimensions and in real-time. Using murine models of infection, we have been able to determine the spatial organization of two bacterial strains found in the oral cavity microbiome. Using confocal microscopy in combination with high-throughput genomic techniques, we have been able to learn more about how bacteria interact within an abscess infection and cause disease.