Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway.

The arginine dihydrolase pathway ( arc operon) is present in a minority of diverse human gut species and enables arginine catabolism. We lack a quantitative understanding of the role of this specialized metabolic pathway in the human gut microbiome. We investigate the role of the arc operon in probiotic E. coli Nissle 1917 on community assembly and health-relevant metabolite production in vitro and in murine gut. The arc operon shapes community assembly and can enhance butyrate production at physiologically relevant environmental pH levels in vitro . In the presence of the arc operon, human gut communities display reduced variability in composition in response to variations in initial pH. Dynamic computational modeling of community assembly reveals the extent of pH-mediated inter-species interactions. Overall, we demonstrate that a specialized metabolic pathway can serve as the control knob of community assembly and beneficial metabolite production.