Rapid identification of pathogenic bacteria is a persistent problem for public health monitoring, food and beverage preparation, and medical response. By growing bacterial species in a defined growth media, where all components and their concentrations are known, species-specific metabolic profiles can be exploited as a means of identifying/differentiating pathogenic vs. non-pathogenic bacteria based on their unique waste products. While infrared spectroscopy techniques offer many advantages in chemical analysis such as minimal sample preparation, low sample volumes, and highly accurate results, chemical and spectral similarities in sample sets can make the application of these techniques difficult. In this study, a defined media (M1) was formulated and compared against commercial tryptic soy broth (TSB), to understand variations in metabolic processes. Attenuated Total Reflectance-FTIR (ATR), diffuse reflectance (DRIFTS), mass spectrometry, and optical density measurements (OD600) were used to determine spectral signatures, identify metabolites, and track the stages of the bacterial growth cycle in Burkholderia pseudomallei, Burkholderia thailandensis, and Yersinia pestis supernatants. This work aims to advance the use of IR-based spectroscopy tools for rapid chemical screening.