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, with Bacteroides thetaiotaomicron converting it into the deaminated nucleobases uracil and xanthine. Using genetic and biochemical approaches, we identify ddbABCDEF, a six-gene locus encoding secreted nucleases and an outer membrane transporter, essential for exogenous DNA metabolism in B. thetaiotaomicron. Colonization of gnotobiotic mice with ddbABCDEF mutants reveals that this pathway significantly alters nucleobase pools in the gut. Comparative genomics demonstrate that ddbABCDEF is 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. SIGNIFICANCE STATEMENTThe gut microbiome plays a crucial role in nutrient metabolism, yet the fate of extracellular DNA within this ecosystem remains poorly understood. This study identifies Bacteroidales species that actively metabolize extracellular DNA, revealing a conserved pathway that converts DNA-derived nucleotides into deaminated nucleobases. We show that Bacteroides thetaiotaomicron utilizes a specialized genetic locus, ddbABCDEF, to facilitate this process, influencing nucleobase availability in the gut. Comparative genomic analyses suggest that ddbABCDEF is evolutionarily linked to bacterial natural transformation systems but has diverged into distinct metabolic subtypes. These findings establish DNA as a metabolic substrate in the gut microbiome, with potential implications for microbial ecology, host-microbe interactions, and gut health.