All bacteria utilize the glycopeptide polymer peptidoglycan to shield themselves from environmental stress. Although often thought of as a "conserved" feature of the cell wall, peptidoglycan exhibits multiple levels of structural heterogeneity across our microbiota. Different bacteria use unique combinations of building blocks to assemble the biopolymer as well as collections of enzymes to remodel the scaffold during growth and division. This degradative process leads to a plethora of individual repeating units, which may escape the bacterium and activate host innate immune pathways. Here, I will present our laboratory's efforts to understand and exploit this complex process to controllably modulate host immune signaling. I will describe our interdiscplinary approaches to identify new enzymes of interest, characterize their activity, and profile strain-specific activation of host organisms. Through these methods, we aim to understand the "rules" of peptidoglycan metabolism in complex communities, which may allow us to better predict the ability of an individual's microbiota to generate bioactive molecules and prime host immunity.