Uric acid-inducible genes in bacteria from the human gut microbiome

Approximately 15% of US adults have circulating levels of uric acid above its solubility limit, which is causally linked to the inflammatory disease gout. In most mammals, uric acid elimination is facilitated by the enzyme uricase. However, human uricase is a pseudogene, having been inactivated early in hominid evolution. Though it has long been known that a substantial amount of uric acid is eliminated in the gut, the role of the gut microbiota in hyperuricemia has not been studied. Here we identify a gene cluster, widely distributed in the gut microbiome, that encodes a pathway for uric acid degradation. Stable isotope tracing demonstrates that gut bacteria metabolize uric acid to xanthine or short chain fatty acids such as acetate, lactate and butyrate. Ablation of the microbiota in uricase-deficient mice causes profound hyperuricemia, and anaerobe-targeted antibiotics increase the risk of gout in humans. These data reveal a role for the gut microbiota in uric acid excretion and highlight the potential for microbiome-targeted therapeutics in hyperuricemia. To investigate which genes are induced by uric acid for anaerobically grown gut bacteria in pure culture. Clostridium sporogenes ATCC 14479, Collinsella aerofaciens ATCC 25986, and Lacrimispora saccharolyticum WM1 treated with uric acid or untreated. Clostridium sporogenes ATCC 14479, Collinsella aerofaciens ATCC 25986, and Lacrimispora saccharolyticum WM1 were streaked from frozen stocks onto blood agar plates. Three individual colonies were selected for each bacterium and were inoculated into separate overnight cultures in Mega medium. The following day, each culture was precultured in Mega medium, and after three hours diluted to an OD of 0.1 into two experimental cultures, one containing standard Mega medium and one with Mega medium containing 5 mM uric acid. Bacteria were allowed to grow until reaching an OD that was commensurate with approximately 50% uric acid degradation as determined by previous experiments. Cell cultures were then combined with two volumes of RNAprotect (Qiagen) in an anaerobic chamber, mixed thoroughly and then allowed to sit for five minutes. Cells were then centrifuged (5,000 x g, 4 °C, 10 min) and the supernatant was decanted. Cells were then subjected to lysozyme digestion, Proteinase K digestion and mechanical disruption with a mixer mill (RETSCH MM400) at 4 °C, 25/s, for 30 min. RNA was then purified using RNeasy kit (Qiagen), followed by DNase digestion and second RNA purification step using the RNeasy kit (Qiagen). RNA integrity was determined using a bioanalyzer (Agilent) and RNA-seq was performed by the Roy J. Carver Biotechnology Center at the University of Illinois.