Basic Science: Stones

Moderated Poster Session

MP2-9 - Identification of an Oxalate Microbiome in the Intestinal Microbiome of Non-Kidney Stone Forming Individuals

Thursday, September 20
4:00 PM - 6:00 PM
Location: Room 242B

Introduction & Objective : The incidence of urinary stone disease (USD) is rapidly increasing, with oxalate being a primary constituent of approximately 80% of all kidney stones.  Despite the high dietary exposure to oxalate by many individuals and its potential nephrotoxicity, mammals do not produce the enzymes to metabolize this compound, instead relying in part on bacteria within the gut to reduce oxalate absorption and urinary excretion.  While considerable research has focused on isolated species of oxalate-degrading bacteria, particularly those with an absolute requirement for oxalate, recent studies have pointed to broader roles for microbiota both in oxalate metabolism and inhibition of urinary stone disease.  We examined the gut microbiota from patients with USD and live-in controls without USD to determine if healthy individuals harbored a more extensive microbial network associated with oxalate metabolism. 


Methods : Recurrent kidney stone formers (patients, n=17) and their non-stone-forming co-habitating partners (controls, n=17) were selected for this 16S rRNA gene metagenomics study. Stool samples were collected, DNA extracted and a 16S rRNA gene library was prepared using appropriate forward and reverse primers. The 16S rRNA gene pooled library was then sequenced on an Ilumina MiSeq platform. All comparative analyses were performed using QIIME. 


Results : Our results show that bacteria enriched in healthy patients largely overlapped with those that correlate with Oxalobacter formigenes, a species presumed to be at the center of an oxalate metabolizing microbial network.  Furthermore, differential abundance analyses identified multiple taxa known to also be stimulated by oxalate in rodent models. Interestingly, the presence of these taxa distinguished patients from healthy controls better than either the relative abundance or colonization of O. formigenes


Conclusions : Our results suggest that healthy oxalate homeostasis in the gastrointestinal tract may not be attributed to the action of O. formigenes alone, but rather involves a collaborative effort between numerous bacterial species. This is the first body of work to show the presence and role of an oxalate microbiome associated with a balanced oxalate homeostasis in non-stone forming individuals.

Dirk Lange

Associate Professor
Dept. of Urologic Sciences, University of British Columbia

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    Aaron Miller

    Project Scientist
    Cleveland Clinic Foundation

    My name is Aaron W. Miller, Ph.D., a project scientist at Cleveland Clinic Foundation. My research focuses on interactions between the microbiome and urinary stone disease specifically for the development of a suite of bacteriotherapies designed to prevent urinary stone disease.

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      Kristina L. Penniston

      Senior Scientist
      University of Wisconsin School of Medicine and Public Health, Department of Urology

      Kristina Penniston is a scientist and registered dietitian nutritionist in Madison, Wisconsin. Dr. Penniston earned her PhD in nutritional science from the University of Wisconsin-Madison. She completed a dietetic internship at the University of Wisconsin Hospital and Clinics and is a certified dietitian member and fellow of the Academy of Nutrition and Dietetics. Dr. Penniston has provided clinical nutrition services to patients with kidney stones and other urologic diseases, such as urologic cancer and benign urologic conditions, for 20 years. Dr. Penniston's research in the Department of Urology at the University of Wisconsin School of Medicine and Public Health focuses on prevention of kidney stones. Specifically, her research aims to develop and test dietary interventions that prevent or ameliorate recurrent stones; promote patients' self-efficacy in managing their stone disease; and understand and improve patients’ health-related quality of life. Dr. Penniston has developed a porcine model of dietary-induced calcium oxalate urolithiasis as a platform for studying dietary influences on stone formation. She also helped to develop the Wisconsin Stone Quality of Life questionnaire, a stone-specific instrument to assess patients' health-related quality of life. Dr. Penniston is a member of the American Urological Association and is a former research scholar (2008-2010). She has been a member of the Research on Calculus Kinetics (ROCK) Society since 2008 and was elected in 2018 as secretary/treasurer. Dr. Penniston publishes regularly in urologic and nutrition journals.

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