Live Gut Microbiome: Cryopreservation and Assays

The gut microbiome plays a central role in host responses to dietary, pharmaceutical, and environmental exposures, yet capturing its functional activity ex vivo remains a major challenge. We developed RapidAIM, a high-throughput assay that maintains live human gut microbiomes in 96-well format, enabling systematic screening of the effects of xenobiotics, prebiotics, and nutritional compounds. RapidAIM preserves taxonomic diversity and functional activity, providing reproducible insights into compound–microbiome interactions and has been shown to reproduce effects observed in vivo. To support longitudinal and large-scale applications, we have established protocols for cryopreservation of live gut microbiomes, which maintain the composition, function, and metabolic output of the microbiome after storage. Together, these innovations provide a robust platform for precision microbiome research, enabling reproducible, scalable investigations of how interventions shape microbial ecology and function.