DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales

The human gut microbiome plays a central role in nutrient metabolism, yet the fate of exogenous nucleic acids within this ecosystem remains poorly understood. Here, we show that multiple Bacteroidales species efficiently metabolize exogenous DNA, withBacteroides thetaiotaomicronconverting it into the deaminated nucleobases uracil and xanthine. Using genetic and biochemical approaches, we identifyddbABCDEF, a six-gene locus encoding secreted nucleases and an outer membrane transporter, essential for exogenous DNA metabolism inB. thetaiotaomicron. Colonization of gnotobiotic mice withddbABCDEFmutants reveals that this pathway significantly alters nucleobase pools in the gut. Comparative genomics demonstrate thatddbABCDEFis evolutionarily related to a natural transformation system present in Bacteroidota and has diversified into four distinct subtypes, each linked to unique DNA-processing activities in closely related gut Bacteroidales strains. These findings thus establish DNA as a metabolic substrate in the gut microbiome and reveal a distinctive pathway for nucleobase production with implications for host-microbe interactions.