, Volume 44, Issue 5, pp 399–407 | Cite as

Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers

  • Joshua M. SternEmail author
  • Saman Moazami
  • Yunping Qiu
  • Irwin Kurland
  • Zigui Chen
  • Ilir Agalliu
  • Robert Burk
  • Kelvin P. Davies
Original Paper


The trillions of microbes that colonize our adult intestine are referred to as the gut microbiome (GMB). Functionally it behaves as a metabolic organ that communicates with, and complements, our own human metabolic apparatus. While the relationship between the GMB and kidney stone disease (KSD) has not been investigated, dysbiosis of the GMB has been associated with diabetes, obesity and cardiovascular disease. In this pilot study we sought to identify unique changes in the GMB of kidney stone patients compared to patients without KSD. With an IRB-approved protocol we enrolled 29 patients into our pilot study. 23 patients were kidney stone formers and six were non-stone forming controls. Specimens were collected after a 6h fast and were flash frozen in dry ice and then stored at −80 °C. Microbiome: determination of bacterial abundance was by analysis of 16 s rRNA marker gene sequences using next generation sequencing. Sequencing of the GMB identified 178 bacterial genera. The five most abundant enterotypes within each group made up to greater than 50 % of the bacterial abundance identified. Bacteroides was 3.4 times more abundant in the KSD group as compared to control (34.9 vs 10.2 %; p = 0.001). Prevotella was 2.8 times more abundant in the control group as compared to the KSD group (34.7 vs 12.3 %; p = 0.005). In a multivariate analysis including age, gender, BMI, and DM, kidney stone disease remained an increased risk for high prevalence for Bacteroides (OR = 3.26, p = 0.033), whereas there was an inverse association with Prevotella (OR = 0.37, p = 0.043). There were no statistically significant differences in bacterial abundance levels for Bacteroides or Prevotella when comparing patients with and without DM, obesity (BMI >30), HTN or HLD. 11 kidney stone patients completed 24 h urine analysis at the time of this writing. Looking at the bacterial genuses with at least 4 % abundance in the kidney stone group, Eubacterium was inversely correlated with oxalate levels (r = −0.60, p < 0.06) and Escherichia trended to an inverse correlation with citrate (r = −0.56, p < 0.08). We also compared bacterial abundance between uric acid (UA) stone formers (n = 5) and non UA stone formers (n = 18) and found no significant difference between them. We identified two genus of bacteria in the GMB that had significant association with KSD. Interestingly, components of the 24-h urine appear to be correlated to bacterial abundance. These preliminary studies for the first time associate differences in the GMB with kidney stone formation. Further studies are warranted to evaluate the potential causative role of preexisting dysbiosis in kidney stone disease.


Nephrolithiasis Kidney stones Gut microbiome Urolithiasis 


Compliance with ethical standards


This study was funded by The Montefiore Department of Urology.

Conflict of interest

The authors declare that they have no conflict of interest.


No animal use for this paper.

Ethical approval

All specimen retrieval involving human participants were in accordance with the ethical standards of the Albert Einstein College of medicine institutional review board with approval number 2014-3487 and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study. Consent was approved by the Albert Einstein College of medicine institutional review board with approval number 2014-3487.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Joshua M. Stern
    • 1
    Email author
  • Saman Moazami
    • 1
  • Yunping Qiu
    • 2
  • Irwin Kurland
    • 2
  • Zigui Chen
    • 3
  • Ilir Agalliu
    • 4
  • Robert Burk
    • 5
  • Kelvin P. Davies
    • 1
  1. 1.Department of UrologyAlbert Einstein College of Medicine, Montefiore Medical Center, Greene Medical Arts PavilionBronxUSA
  2. 2.Department of MedicineAlbert Einstein College of MedicineBronxUSA
  3. 3.Department of MicrobiologyThe Chinese University of Hong KongHong KongChina
  4. 4.Department of EpidemiologyAlbert Einstein College of MedicineBronxUSA
  5. 5.Department of MicrobiologyAlbert Einstein College of MedicineBronxUSA

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