We established a proprietary fluorescence microscopy-based profiling technology (Woehrstein et al., Science Advances, 2017) with a combination of superior precision, sensitivity, taxonomic depth and quantification properties. With our multiplexing panels, we can rapidly and accurately decipher the in vivo microbiome composition of a human sample. These data are critical to better inform the selection of the optimal microbial strains for complex consortia with tailored disease-targeting properties and a superior efficacy and safety profile.