Adaptive evolution identifies candidate genetic routes associated with oxalate utilization in probiotic and gut-derived E.coli

Functional probiotics offer a therapeutic modality for degrading disease-associated compounds in the gut. In hyperoxaluria, therapeutic strategies based on natural oxalate degraders such as Oxalobacter formigenes have shown variable efficacy, motivating methods to expand the repertoire of oxalate-utilizing bacterial chassis and explore native genetic routes by which this function can evolve. Here, we used adaptive laboratory evolution (ALE) under microaerobic conditions to enable oxalate utilization in probiotic Escherichia coli Nissle 1917 and three gut-derived E. coli isolates. Within ∼400 generations, all lines evolved robust growth on minimal medium with oxalate as the sole carbon and energy source. Recurrent mutations identify native aldehyde-dehydrogenase-associated modules, including AdhE and the Eut system, as candidate genetic routes associated with evolved oxalate utilization. We propose ALE as a scalable framework to uncover latent metabolic potential in probiotic and gut-associated bacteria and generate mechanistically tractable candidates for downstream functional validation.