Mechanisms of the intestinal and urinary microbiome in kidney stone disease

Miller, Aaron W.; Penniston, Kristina L.; Fitzpatrick, Kate; Agudelo, José; Tasian, Gregory; Lange, Dirk

doi:10.1038/s41585-022-00647-5

Cited by 89Kidney Stones and Urolithiasis TreatmentsGut microbiota and healthUrinary Tract Infections Management

Mechanisms of the intestinal and urinary microbiome in kidney stone disease

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Miller, Aaron W., Penniston, Kristina L., Fitzpatrick, Kate, Agudelo, José, Tasian, Gregory, Lange, Dirk·2022·Nature Reviews Urology

DOI 10.1038/s41585-022-00647-5PMC PMC11234243

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Abstract

Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.

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Lack of a "healthy" microbiota is associated with many forms of disease, including metabolic diseases, gastrointestinal cancer, inflammatory bowel disease, renal disease, and neurodegenerative diseases associated with aging.
“Lack of a “healthy” microbiota is associated with many forms of disease (19–24), such as metabolic diseases (obesity, type 2 diabetes), gastrointestinal cancer, inflammatory bowel disease, and renal disease, as well as neurodegenerative diseases (NDs) associated with aging, in which the activity and composition of the gut microbiota change during the life cycle.”
From Modulation of the gut–brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis (2023) · cites this paper as [22]

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The association between bacteria and urinary stones
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Defining Dysbiosis in Patients with Urolithiasis
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Genetic and microbiome influence on lipid metabolism and dyslipidemia
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Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures
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Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis
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A randomised Phase II/III study to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria
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Understanding the host-microbe interactions using metabolic modeling
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The Metabolic and Ecological Interactions of Oxalate-Degrading Bacteria in the Mammalian Gut
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Intestinal hyperabsorption of oxalate in calcium oxalate stone formers: application of a new test with [13C2]oxalate.
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Bacteria can promote calcium oxalate crystal growth and aggregation
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Antibiotic prescribing frequency amongst patients in primary care: a cohort study using electronic health records
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Role of Oxalobacter formigenes in Calcium Oxalate Stone Disease: A Study from North India
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The role of intestinal oxalate transport in hyperoxaluria and the formation of kidney stones in animals and man
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The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease
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A randomised Phase I/II trial to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria
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Role of the Lower and Upper Intestine in the Production and Absorption of Gut Microbiota-Derived PUFA Metabolites
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Oxalate-Degrading Activity inBifidobacterium animalissubsp.lactis: Impact of Acidic Conditions on the Transcriptional Levels of the Oxalyl Coenzyme A (CoA) Decarboxylase and Formyl-CoA Transferase Genes
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The microbiome of calcium-based urinary stones
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Probiotics in Extraintestinal Diseases: Current Trends and New Directions
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Lactobacillus acidophilus stimulates the expression of SLC26A3 via a transcriptional mechanism
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Profiling the urinary microbiome in men with calcium-based kidney stones
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Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease
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Human kidney stones: a natural record of universal biomineralization
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Factors Related to Colonization with Oxalobacter formigenes in U.S. Adults
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The role of fluid intake in the prevention of kidney stone disease: A systematic review over the last two decades
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Transcellular oxalate and Cl−absorption in mouse intestine is mediated by the DRA anion exchanger Slc26a3, and DRA deletion decreases urinary oxalate
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Geobiology reveals how human kidney stones dissolve in vivo
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Cellular distributions of monocarboxylate transporters: a review
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Probiotic-induced reduction of gastrointestinal oxalate absorption in healthy subjects
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Bioactive substances of plant origin in food - impact on genomics
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Apical NHE isoforms differentially regulate butyrate-stimulated Na absorption in rat distal colon
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Gut microbiota and oxalate homeostasis
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Antibiotic Use and Risk of Incident Kidney Stones in Female Nurses
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Sensitivity of Human Strains of Oxalobacter formigenes to Commonly Prescribed Antibiotics
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Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation
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Flagellum Is Responsible for Promoting Effects of Viable Escherichia coli on Calcium Oxalate Crystallization, Crystal Growth, and Crystal Aggregation
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Effects of Prebiotic Fiber Xylooligosaccharide in Adenine‐Induced Nephropathy in Mice
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The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species
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Roles of short-chain fatty acids in kidney diseases
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Regulation of the rat NHE3 gene promoter by sodium butyrate
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Effects of Lactobacillus casei and Bifidobacterium breve on urinary oxalate excretion in nephrolithiasis patients
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Molecular cloning and promoter analysis of downregulated in adenoma (DRA)
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Calcium Oxalate Urolithiasis: A Case of Missing Microbes?
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Animal models of naturally occurring stone disease
Alford, A. V., Furrow, E., Borofsky, M. S., & Lulıch, J. P. (2020) · Nature Reviews Urology · doi:10.1038/s41585-020-00387-4 · Cited by 48 · see citing works
Improving Treatment Options for Primary Hyperoxaluria
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Evaluation of Biofilm Induced Urinary Infection Stone Formation in a Novel Laboratory Model System
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Consumption of Cooked Black Beans Stimulates a Cluster of Some Clostridia Class Bacteria Decreasing Inflammatory Response and Improving Insulin Sensitivity
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Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet
Miller, A. W., Orr, T. J., Dearing, M. D., & Monga, M. (2019) · The ISME Journal · doi:10.1038/s41396-019-0357-4 · Cited by 38 · see citing works
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Acute probiotic ingestion reduces gastrointestinal oxalate absorption in healthy subjects
Al-Wahsh, I. A., Wu, Y., & Liebman, M. (2011) · Urological Research · doi:10.1007/s00240-011-0421-7 · Cited by 37 · see citing works
1H NMR-based metabolomic study of metabolic profiling for the urine of kidney stone patients
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Oxalobacter formigenes: Opening the door to probiotic therapy for the treatment of hyperoxaluria
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Fecal transplant modifies urine chemistry risk factors for urinary stone disease
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Microbiota Diversification and Crash Induced by Dietary Oxalate in the Mammalian Herbivore Neotoma albigula
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Associations between UK tap water and gut microbiota composition suggest the gut microbiome as a potential mediator of health differences linked to water quality
Bowyer, R. C. E., Schillereff, D. N., Jackson, M. A., Roy, C. I. L., Wells, P. M., Spector, T. D., & Steves, C. J. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.139697 · Cited by 27 · see citing works
Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease
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In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis
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Equol, via Dietary Sources or Intestinal Production, May Ameliorate Estrogen Deficiency-Induced Bone Loss
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Hemostasis in Children With Dysbacteriosis in Chronic Constipation
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Oxalate nephropathy from cashew nut intake
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Modulation of the gut–brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis
Hong, D., Zhang, C., Wu, W., Lu, X., & Zhang, L. (2023) · Frontiers in Neurology · doi:10.3389/fneur.2023.1133546 · Cited by 38 · see citing works

BMC322- A RATIONALLY-DESIGNED LIVE BACTERIAL CONSORTIUM BASED ON MICROBIOME FUNCTIONAL GENOMIC ANALYSIS FOR TREATMENT OF IBD
Polonsky, O., Meshner, S., Eshar, S., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.140 · Cited by 1 · see citing works
Sa1911 – Analysis of the Small Intestinal Microbiome Reveals Marked Differences from Stool Microbiome in a Large Scale Human Cohort: Redefining the “Gut Microbiome”
Leite, G., Weitsman, S. R., Celly, S., et al. (2019) · Gastroenterology · doi:10.1016/s0016-5085(19)37977-6 · Cited by 5 · see citing works
Determining the true burden of kidney stone disease
Thongprayoon, C., Krambeck, A. E., & Rule, A. D. (2020) · Nature Reviews Nephrology · doi:10.1038/s41581-020-0320-7 · Cited by 425 · see citing works
Why targeting the microbiome is not so successful: can randomness overcome the adaptation that occurs following gut manipulation?
Ilan, Y. (2019) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s203823 · Cited by 76 · see citing works
The Impact of Bilateral Stone Disease on Patients' Disease Progression and Health-Related Quality of Life
Raizenne, B. L., Deyirmendjian, C., Lafontaine, M.-L., et al. (2023) · Journal of Endourology · doi:10.1089/end.2023.0132 · Cited by 9 · see citing works

Authors: Miller, A. W., Penniston, K. L., Fitzpatrick, K., Agudelo, J., Tasian, G., & Lange, D.
Affiliations: Cleveland Clinic (US)
University of Wisconsin–Madison (US)
Children's Hospital of Philadelphia (US)
University of British Columbia (CA)
Corresponding author: Lange, Dirk
ORCID: Miller, Aaron W.
Penniston, Kristina L.
Agudelo, José
Tasian, Gregory
Lange, Dirk
Venue: Nature Reviews Urology
Publisher: Springer Science and Business Media LLC
Published: 2022-09-20
Volume: 19
Issue: 12
Pages: 695-707
ISSN: 1759-4812 (ISSN-L)
1759-4820
DOI: 10.1038/s41585-022-00647-5
PMC: PMC11234243
OpenAlex: W4296774973
Cited by: 89
References: 166
Citations by year: 2026: 16 · 2025: 30 · 2024: 29 · 2023: 13 · 2022: 1
FWCI: 3.16
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Reviews Urology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of Diabetes and Digestive and Kidney Diseases (R01DK121689)
Topics: Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Kidney Stones and Urolithiasis Treatments
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Epidemiology › Urinary Tract Infections Management
Keywords: kidney stones, gut microbiota, urinary microbiome, oxalate homeostasis, oxalate absorption, stone growth, metabolic syndrome
MeSH terms: Gastrointestinal Microbiome, Humans, Kidney, Kidney Calculi, Oxalates, Incidence

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Mechanisms of the intestinal and urinary microbiome in kidney stone disease

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