Selective capture, isolation, and characterization of mucin foraging neu-raminidase-active bacteria from microbiomes using a non-inhibitory activ-ity-based probe

Neuraminidase is expressed by some bacteria in host-associated environments to cleave terminal sialic acid residues from mucin layers. This activity has been associated with nutrient acquisition, biofilm formation, and host infection, and is more prevalent in pathogens than commensal microbes. Since the integrity of the mucin layer in the airway and gastrointestinal tracts is a crucial part of the immune system, bacteria that degrade it through neuraminidase activity are of interest. We de-signed an activity-based probe (Neu-BDP) to detect neuraminidase-expressing bacteria without impacting functional activity. We show that by utilizing a quinone methide-based covalent trapping mechanism, Neu-BDP avoids inhibition of neuramini-dase while still maintaining high selectivity for target microbes. We envision that this approach for whole cell neuraminidase detection will enable future investigation of microbes associated with infection and colonization of the gut, airway, and other mucosal surfaces.