Essential metal ions like zinc, copper, and iron have a broad range of signaling, stabilizing, and catalytic functions across all living systems. The gut microbiota typically acquires these metals through the host diet but must be able to adapt to dietary fluctuations. Many studies link changes in available metal nutrients to alterations in bacterial colonization, pathogen resistance, and gut microbiota community composition but the underlying mechanisms remain unclear. Our research program revolves around elucidating fundamental molecular mechanisms by which metals affect the microbiota. This talk will focus on our efforts to develop metal ion biosensors for illuminating metals within complex bacterial communities. We are investigating a series of cofactor-based fluorescent proteins that emit wavelengths ranging from green to the near-infrared and which, unlike green fluorescent proteins and their variants, do not rely on oxygen. I will cover how our group is re-engineering these proteins to develop novel sensors for zinc and copper. Application of these sensors to live bacteria and opportunities for their use in gut microbiota models will be discussed. I will also present our progress investigating how metal ions affect growth and cell interactions of the Lactobacillaceae family of bacteria, which are crucial members of the gut microbiota.