Hill, N. R. et al. Global prevalence of chronic kidney disease – a systematic review and meta-analysis. PLoS ONE 11, e0158765 (2016).
Google Scholar
Snelson, M. et al. A renal clinician’s guide to the gut microbiota. J. Ren. Nutr. 30, 384–395 (2020).
Google Scholar
Lambert, K. et al. Targeting the gut microbiota in kidney disease: the future in renal nutrition and metabolism. J. Ren. Nutr. 33, S30–S39 (2023).
Google Scholar
Stanford, J. et al. The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature. BMC Nephrol. 21, 215 (2020).
Google Scholar
Holle, J. et al. Inflammation in children with CKD linked to gut dysbiosis and metabolite imbalance. J. Am. Soc. Nephrol. 33, 2259–2275 (2022).
Google Scholar
Holle, J. et al. Gut microbiome alterations precede graft rejection in kidney transplantation patients. Am. J. Transpl. 18, S1600–S6135 (2025).
Vaziri, N. D. et al. Chronic kidney disease alters intestinal microbial flora. Kidney Int. 83, 308–315 (2013).
Nishiyama, K. et al. Chronic kidney disease after 5/6 nephrectomy disturbs the intestinal microbiota and alters intestinal motility. J. Cell Physiol. 234, 6667–6678 (2019).
Google Scholar
Mishima, E. et al. Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model. Am. J. Physiol. Renal Physiol. 315, F824–F833 (2018).
Google Scholar
Vaziri, N. D., Yuan, J. & Norris, K. Role of urea in intestinal barrier dysfunction and disruption of epithelial tight junction in chronic kidney disease. Am. J. Nephrol. 37, 1–6 (2013).
Google Scholar
Chaves, L. D. et al. Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis. Am. J. Physiol. Renal Physiol. 315, F487–F502 (2018).
Google Scholar
Wong, J. et al. Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD. Am. J. Nephrol. 39, 230–237 (2014).
Google Scholar
Wang, X. et al. Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents. Gut 69, 2131–2142 (2020).
Google Scholar
Laiola, M. et al. Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study. Gut (2025).
Noel, S. et al. Gut microbiota-immune system interactions during acute kidney injury. Kidney360 2, 528–531 (2021).
Google Scholar
Noel, S. et al. Metagenomic sequencing reveals distinct gut microbiome profiles in patients with AKI compared to CKD and normals: KPMP project. Am. Soc. Neph. (2024).
Mishima, E. et al. Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS-based metabolomics approach. Kidney Int. 92, 634–645 (2017).
Google Scholar
Avery, E. G. et al. Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage. Cardiovasc. Res. 119, 1441–1452 (2023).
Google Scholar
Jang, H. R. et al. Early exposure to germs modifies kidney damage and inflammation after experimental ischemia-reperfusion injury. Am. J. Physiol. Renal Physiol. 297, F1457–F1465 (2009).
Google Scholar
Al, K. F. et al. Multi-site microbiota alteration is a hallmark of kidney stone formation. Microbiome 11, 263 (2023).
Google Scholar
Moore, B. N. et al. Commensal microbiota regulate aldosterone. Am. J. Physiol. Renal Physiol. 326, F1032–F1038 (2024).
Google Scholar
Moore, B. N. & Pluznick, J. L. Commensal microbiota regulate renal gene expression in a sex-specific manner. Am. J. Physiol. Renal Physiol. 324, F511–F520 (2023).
Google Scholar
Xu, J. et al. Microbes regulate glomerular filtration rate in health and chronic kidney disease in mice. Prerit at bioRxiv (2025).
Gupta, N. et al. Targeted inhibition of gut microbial trimethylamine N-oxide production reduces renal tubulointerstitial fibrosis and functional impairment in a murine model of chronic kidney disease. Arterioscler. Thromb. Vasc. Biol. 40, 1239–1255 (2020).
Google Scholar
Wang, M. et al. The gut microbial metabolite trimethylamine N -oxide, incident CKD, and kidney function decline. J. Am. Soc. Nephrol. 35, 749–760 (2024).
Google Scholar
Andrikopoulos, P. et al. Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. Nat. Commun. 14, 5843 (2023).
Google Scholar
Witkowski, M., Weeks, T. L. & Hazen, S. L. Gut microbiota and cardiovascular disease. Circ. Res. 127, 553–570 (2020).
Google Scholar
Holle, J. et al. Gut dysbiosis contributes to TMAO accumulation in CKD. Nephrol. Dial. Transpl. 39, 1923–1926 (2024).
Google Scholar
Gryp, T. et al. Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease. Kidney Int. 97, 1230–1242 (2020).
Google Scholar
Agudelo, J. & Miller, A. W. A perspective on the metabolic potential for microbial contributions to urolithiasis. Kidney360 2, 1170–1173 (2021).
Google Scholar
Miller, A. W. et al. Mechanisms of the intestinal and urinary microbiome in kidney stone disease. Nat. Rev. Urol. 19, 695–707 (2022).
Google Scholar
Stepanova, N. Role of impaired oxalate homeostasis in cardiovascular disease in patients with end-stage renal disease: an opinion article. Front. Pharmacol. 12, 692429 (2021).
Google Scholar
Nazzal, L., Puri, S. & Goldfarb, D. S. Enteric hyperoxaluria: an important cause of end-stage kidney disease. Nephrol. Dialysis Transplant. 31, 375–382 (2015).
David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).
Google Scholar
Tang, W. H. W. & Hazen, S. L. Unraveling the complex relationship between gut microbiome and cardiovascular diseases. Circulation 149, 1543–1545 (2024).
Google Scholar
Johnson, A. J. et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe 25, 789–802.e5 (2019).
Google Scholar
Mailing, L. J. et al. Exercise and the gut microbiome: a review of the evidence, potential mechanisms, and implications for human health. Exerc. Sport. Sci. Rev. 47, 75–85 (2019).
Vandecruys, M. et al. Revitalizing the gut microbiome in chronic kidney disease: a comprehensive exploration of the therapeutic potential of physical activity. Toxins 16, 242 (2024).
Google Scholar
Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).
Google Scholar
Biruete, A. et al. Phosphate binders and nonphosphate effects in the gastrointestinal tract. J. Ren. Nutr. 30, 4–10 (2020).
Google Scholar
Asnicar, F. et al. Blue poo: impact of gut transit time on the gut microbiome using a novel marker. Gut 70, 1665–1674 (2021).
Google Scholar
O’Donnell, J. A. et al. The gut microbiome and hypertension. Nat. Rev. Nephrol. 19, 153–167 (2023).
Byndloss, M. et al. The gut microbiota and diabetes: research, translation, and clinical applications-2023 diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetes Care 47, 1491–1508 (2024).
Google Scholar
Teixeira, R. R. et al. Gut microbiota profile of patients on peritoneal dialysis: comparison with household contacts. Eur. J. Clin. Nutr. 77, 90–97 (2022).
Poesen, R. et al. The influence of CKD on colonic microbial metabolism. J. Am. Soc. Nephrol. 27, 1389–1399 (2016).
Google Scholar
Wiese, G. N. et al. Gut microbiota and uremic retention solutes in adults with moderate CKD: a 6-day controlled feeding study. J. Ren. Nutr. 34, 26–34 (2023).
Google Scholar
Wu, G. et al. A core microbiome signature as an indicator of health. Cell 187, 6550–6565.e11 (2024).
Google Scholar
Liu, F. et al. Sex-specific dysbiotic bladder microbiome in CKD uncovered via high-throughput sequencing and culture. Preprint at Research Square (2023).
Hrbacek, J. et al. Bladder microbiota are associated with clinical conditions that extend beyond the urinary tract. Microorganisms 10, 874 (2022).
Google Scholar
Kachroo, N. et al. Meta-analysis of clinical microbiome studies in urolithiasis reveal age, stone composition, and study location as the predominant factors in urolithiasis-associated microbiome composition. Mbio 12, e02007-21 (2021).
Google Scholar
Liang, J. & Liu, Y. Animal models of kidney disease: challenges and perspectives. Kidney360 4, 1479–1493 (2023).
Google Scholar
Mirzayi, C. et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nat. Med. 27, 1885–1892 (2021).
Google Scholar
Abdill, R. J., Adamowicz, E. M. & Blekhman, R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 20, e3001536 (2022).
Google Scholar
Muralitharan, R. R. et al. Guidelines for microbiome studies in renal physiology. Am. J. Physiol. Renal Physiol. 325, F345–F362 (2023).
Google Scholar
Wensel, C. R. et al. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J. Clin. Invest. 132, e154944 (2022).
Google Scholar
Nasko, D. J. et al. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biol. 19, 165 (2018).
Google Scholar
Smith, R. H. et al. Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome. Anim. Microbiome 4, 57 (2022).
Google Scholar
Mills, S. et al. Precision nutrition and the microbiome, part I: current state of the science. Nutrients 11, 1468 (2019).
Google Scholar
Sommer, F. & Bäckhed, F. The gut microbiota — masters of host development and physiology. Nat. Rev. Microbiol. 11, 227–238 (2013).
Google Scholar
Walter, J. & Ley, R. The human gut microbiome: ecology and recent evolutionary changes. Annu. Rev. Microbiol. 65, 411–429 (2011).
Google Scholar
Meijers, B., Evenepoel, P. & Anders, H. J. Intestinal microbiome and fitness in kidney disease. Nat. Rev. Nephrol. 15, 531–545 (2019).
Mulle, J. G., Sharp, W. G. & Cubells, J. F. The gut microbiome: a new frontier in autism research. Curr. Psychiatry Rep. 15, 337 (2013).
Google Scholar
Pluznick, J. L. The gut microbiota in kidney disease. Science 369, 1426–1427 (2020).
Google Scholar
Harrison, M. A. et al. Production of p-cresol by decarboxylation of p-HPA by all five lineages of Clostridioides difficile provides a growth advantage. Front. Cell. Infect. Microbiol. 11, 757599 (2021).
Google Scholar
Fishbane, S. N. & Nigwekar, S. Phosphate absorption and hyperphosphatemia management in kidney disease: a physiology-based review. Kidney Med. 3, 1057–1064 (2021).
Google Scholar
Weiner, I. D., Mitch, W. E. & Sands, J. M. Urea and ammonia metabolism and the control of renal nitrogen excretion. Clin. J. Am. Soc. Nephrol. 10, 1444–1458 (2015).
Google Scholar
Tonelli, M., Karumanchi, S. A. & Thadhani, R. Epidemiology and mechanisms of uremia-related cardiovascular disease. Circulation 133, 518–536 (2016).
Google Scholar
Chen, Y. et al. Kidney clearance of secretory solutes is associated with progression of CKD: the CRIC study. J. Am. Soc. Nephrol. 31, 817–827 (2020).
Google Scholar
Chen, Y. et al. Association of tubular solute clearances with the glomerular filtration rate and complications of chronic kidney disease: the chronic renal insufficiency cohort study. Nephrol. Dial. Transpl. 36, 1271–1281 (2020).
Lim, Y. J. et al. Uremic toxins in the progression of chronic kidney disease and cardiovascular disease: mechanisms and therapeutic targets. Toxins 13, 142 (2021).
Google Scholar
Owada, S. et al. Indoxyl sulfate reduces superoxide scavenging activity in the kidneys of normal and uremic rats. Am. J. Nephrol. 28, 446–454 (2008).
Google Scholar
Niwa, T. Indoxyl sulfate is a nephro-vascular toxin. J. Ren. Nutr. 20, S2–S6 (2010).
Google Scholar
Liu, W. C., Tomino, Y. & Lu, K. C. Impacts of indoxyl sulfate and p-cresol sulfate on chronic kidney disease and mitigating effects of AST-120. Toxins 10, 367 (2018).
Google Scholar
Al-mansouri, A. et al. Assessment of treatment burden and its impact on quality of life in dialysis-dependent and pre-dialysis chronic kidney disease patients. Res. Soc. Adm. Pharm. 17, 1937–1944 (2021).
Tang, W. H. et al. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circ. Res. 116, 448–455 (2015).
Google Scholar
Meijers, B. K. et al. p-Cresol and cardiovascular risk in mild-to-moderate kidney disease. Clin. J. Am. Soc. Nephrol. 5, 1182–1189 (2010).
Google Scholar
Ren, X. et al. Plasma metabolomics of dietary intake of protein-rich foods and kidney disease progression in children. J. Ren. Nutr. 34, 95–104 (2024).
Google Scholar
Liu, J. et al. Effect of dapagliflozin on proteomics and metabolomics of serum from patients with type 2 diabetes. Diabetol. Metab. Syndr. 15, 251 (2023).
Google Scholar
Koeth, R. A. et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19, 576–585 (2013).
Google Scholar
Tang, W. H. et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N. Engl. J. Med. 368, 1575–1584 (2013).
Google Scholar
Saito, Y. et al. Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites. FEMS Microbiol. Ecol. 94, fiy125 (2018).
Google Scholar
Whittaker, R. Evolution and measurement of species diversity. Taxon 21, 213–251 (1972).
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
Knights, D. et al. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe 10, 292–296 (2011).
Google Scholar
Hu, X. et al. Characterizing the gut microbiota in patients with chronic kidney disease. Postgrad. Med. 132, 495–505 (2020).
Google Scholar
Ren, Z. et al. Alterations of the human gut microbiome in chronic kidney disease. Adv. Sci. 7, 2001936 (2020).
Google Scholar
Yu, W. et al. The gut microbiome in differential diagnosis of diabetic kidney disease and membranous nephropathy. Ren. Fail. 42, 1100–1110 (2020).
Google Scholar
Khasnobish, A. et al. Dysbiosis in the salivary microbiome associated with IgA nephropathy — a Japanese cohort study. Microbes Env. 36, ME21006 (2021).
Du, X. et al. Alteration of gut microbial profile in patients with diabetic nephropathy. Endocrine 73, 71–84 (2021).
Google Scholar
Yu, B. et al. The gut microbiome in microscopic polyangiitis with kidney involvement: common and unique alterations, clinical association and values for disease diagnosis and outcome prediction. Ann. Transl. Med. 9, 1286 (2021).
Google Scholar
Xiang, L. et al. Prediction of the occurrence of calcium oxalate kidney stones based on clinical and gut microbiota characteristics. World J. Urol. 40, 221–227 (2022).
Google Scholar
Shi, X. et al. Alterations of gut microbial pathways and virulence factors in hemodialysis patients. Front. Cell Infect. Microbiol. 12, 904284 (2022).
Google Scholar
Dong, Y. et al. Development and validation of diagnostic models for immunoglobulin A nephropathy based on gut microbes. Front. Cell Infect. Microbiol. 12, 1059692 (2022).
Google Scholar
Tang, Y. et al. Aberrant gut microbiome contributes to barrier dysfunction, inflammation, and local immune responses in IgA nephropathy. Kidney Blood Press. Res. 48, 261–276 (2023).
Google Scholar
Chen, T. H. et al. Exploring the relevance between gut microbiota-metabolites profile and chronic kidney disease with distinct pathogenic factor. Microbiol. Spectr. 11, e0280522 (2023).
Cai, F. et al. Systematic microbiome dysbiosis is associated with IgA nephropathy. Microbiol. Spectr. 11, e0520222 (2023).
Jiang, Y. et al. Combination of the gut microbiota and clinical indicators as a potential index for differentiating idiopathic membranous nephropathy and minimal change disease. Ren. Fail. 45, 2209392 (2023).
Google Scholar
Tang, S. et al. Guild-level signature of gut microbiome for diabetic kidney disease. mBio 15, e0073524 (2024).
Lee, A. M. et al. Using machine learning to identify metabolomic signatures of pediatric chronic kidney disease etiology. J. Am. Soc. Nephrol. 33, 375–386 (2022).
Google Scholar
Hu, J. et al. Location-specific oral microbiome possesses features associated with CKD. Kidney Int. Rep. 3, 193–204 (2017).
Google Scholar
Yang, Y. et al. The genetics of urinary microbiome, an exploration of the trigger in calcium oxalate stone. Front. Genet. 14, 1260278 (2023).
Google Scholar
NIH/FDA. BEST (Biomarkers, EndpointS, and other Tools) Resource. ncbi.nlm.nih.gov (FDA, 2016).
Bennett, M. & Devarajan, P. in Biomarkers of Kidney Disease (ed. Edelstein, C.) 1–24 (Academic, 2011).
Yu, Y. et al. Assessing and mitigating batch effects in large-scale omics studies. Genome Biol. 25, 254 (2024).
Google Scholar
Agudelo, J. et al. Delineating the role of the urinary metabolome in the lithogenesis of calcium-based kidney stones. Urology 167, 49–55 (2022).
Vaswani, A. et al. Attention is all you need. In 31st Conference on Neural Information Processing Systems (NIPS) (eds. Guyon, I. et al.) (2017).
Theodosiou, A. A. & Read, R. C. Artificial intelligence, machine learning and deep learning: potential resources for the infection clinician. J. Infect. 87, 287–294 (2023).
Trepka, K. R. et al. Pharma[e]cology: how the gut microbiome contributes to variations in drug response. Annu. Rev. Pharmacol. Toxicol. 65, 355–373 (2024).
Wallace, B. D. et al. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 330, 831–835 (2010).
Google Scholar
Haiser, H. J. et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295–298 (2013).
Google Scholar
Simpson, J. B. et al. Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate. Gut Microbes 14, 2107289 (2022).
Google Scholar
Yang, T. et al. Identification of a gut commensal that compromises the blood pressure-lowering effect of ester angiotensin-converting enzyme inhibitors. Hypertension 79, 1591–1601 (2022).
Google Scholar
Kyoung, J. & Yang, T. Depletion of the gut microbiota enhances the blood pressure-lowering effect of captopril: implication of the gut microbiota in resistant hypertension. Hypertens. Res. 45, 1505–1510 (2022).
Google Scholar
Vallon, V. & Verma, S. Effects of SGLT2 inhibitors on kidney and cardiovascular function. Annu. Rev. Physiol. 83, 503–528 (2021).
Google Scholar
Billing, A. M. et al. Metabolic communication by SGLT2 inhibition. Circulation 149, 860–884 (2024).
Google Scholar
Chrysopoulou, M. & Rinschen, M. M. Metabolic rewiring and communication: an integrative view of kidney proximal tubule function. Annu. Rev. Physiol. 86, 405–427 (2024).
Google Scholar
Szymczak-Pajor, I. et al. The gut microbiota-related antihyperglycemic effect of metformin. Pharmaceuticals 18, 55 (2025).
Google Scholar
Nigam, S. K. The SLC22 transporter family: a paradigm for the impact of drug transporters on metabolic pathways, signaling, and disease. Annu. Rev. Pharmacol. Toxicol. 58, 663–687 (2018).
Google Scholar
Hakimi, S., Dutta, P. & Layton, A. T. Renal calcium and magnesium handling during pregnancy: modeling and analysis. Am. J. Physiol. Renal Physiol. 327, F77–F90 (2024).
Google Scholar
Stadt, M. M. & Layton, A. T. A modeling analysis of whole body potassium regulation on a high-potassium diet: proximal tubule and tubuloglomerular feedback effects. Am. J. Physiol. Regul. Integr. Comp. Physiol. 326, R401–R415 (2024).
Google Scholar
Jariwala, P. B. et al. Discovering the microbial enzymes driving drug toxicity with activity-based protein profiling. ACS Chem. Biol. 15, 217–225 (2020).
Google Scholar
Rinschen, M. M. et al. Accelerated lysine metabolism conveys kidney protection in salt-sensitive hypertension. Nat. Commun. 13, 4099 (2022).
Google Scholar
Andrade-Oliveira, V. et al. Gut bacteria products prevent AKI induced by ischemia-reperfusion. J. Am. Soc. Nephrol. 26, 1877–1888 (2015).
Google Scholar
Emal, D. et al. Depletion of gut microbiota protects against renal ischemia-reperfusion injury. J. Am. Soc. Nephrol. 28, 1450–1461 (2017).
Google Scholar
Nakade, Y. et al. Gut microbiota-derived D-serine protects against acute kidney injury. JCI Insight 3, e97957 (2018).
Google Scholar
Zhu, H. et al. The probiotic L. casei Zhang slows the progression of acute and chronic kidney disease. Cell Metab. 33, 1926–1942.e8 (2021).
Google Scholar
Yang, Z. et al. The prevention effect of Limosilactobacillus reuteri on acute kidney injury by regulating gut microbiota. Microbiol. Immunol. 68, 213–223 (2024).
Google Scholar
Gharaie, S. et al. Microbiome modulation after severe acute kidney injury accelerates functional recovery and decreases kidney fibrosis. Kidney Int. 104, 470–491 (2023).
Google Scholar
Li, H.-B. et al. Faecalibacterium prausnitzii attenuates CKD via butyrate-renal GPR43 axis. Circulation Res. 131, e120–e134 (2022).
Google Scholar
Shankaranarayanan, D. & Raj, D. S. Gut microbiome and kidney disease: reconciling optimism and skepticism. Clin. J. Am. Soc. Nephrol. 17, 1694–1696 (2022).
Google Scholar
He, M. et al. Gut microbial metabolites SCFAs and chronic kidney disease. J. Transl. Med. 22, 172 (2024).
Google Scholar
Tang, Z., Yu, S. & Pan, Y. The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies. J. Transl. Med. 21, 689 (2023).
Google Scholar
Gao, B. et al. Butyrate producing microbiota are reduced in chronic kidney diseases. Sci. Rep. 11, 23530 (2021).
Google Scholar
Guo, X. et al. Novel metabolites to improve glomerular filtration rate estimation. Kidney Blood Press. Res. 48, 287–296 (2023).
Google Scholar
Yamaguchi, Y. et al. Plasma metabolites associated with chronic kidney disease and renal function in adults from the Baltimore longitudinal study of aging. Metabolomics 17, 1–11 (2021).
Peng, H. et al. A metabolomics study of metabolites associated with the glomerular filtration rate. BMC Nephrol. 24, 105 (2023).
Google Scholar
Li, T. et al. Consistency of metabolite associations with measured glomerular filtration rate in children and adults. Clin. Kidney J. 17, sfae108 (2024).
Google Scholar
Roberts, A. B. et al. Development of a gut microbe-targeted nonlethal therapeutic to inhibit thrombosis potential. Nat. Med. 24, 1407–1417 (2018).
Google Scholar
Graboski, A. L. et al. Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate. Cell Chem. Biol. 30, 1402–1413.e7 (2023).
Google Scholar
Winkler, M. K. H. & van Loosdrecht, M. C. M. Intensifying existing urban wastewater. Science 375, 377–378 (2022).
Google Scholar
Candry, P. et al. Tailoring polyvinyl alcohol-sodium alginate (PVA-SA) hydrogel beads by controlling crosslinking pH and time. Sci. Rep. 12, 20822 (2022).
Google Scholar
Godfrey, B. et al. Co-immobilization of AOA strains with Anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions. Chemosphere 342, 140192 (2023).
Google Scholar
Gottshall, E. Y. et al. Sustained nitrogen loss in a symbiotic association of comammox Nitrospira and anammox bacteria. Water Res. 202, 117426 (2021).
Google Scholar
Landreau, M. et al. Immobilization of active ammonia-oxidizing archaea in hydrogel beads. npj Clean Water 4, 43 (2021).
Google Scholar
Li, B. et al. Mainstream nitrogen removal from low temperature and low ammonium strength municipal wastewater using hydrogel-encapsulated comammox and anammox. Water Res. 242, 120303 (2023).
Google Scholar
Saingam, P. et al. Towards an effective delivery system of a microbial sink of the uremic toxin, p-cresol; an in vitro study with Thauera aminoaromatica S2. Front. Microbiol. 16, 1577556 (2025).
Google Scholar
Ogawa, T. et al. Oral administration of Bifidobacterium longum in a gastro-resistant seamless capsule decreases serum phosphate levels in patients receiving haemodialysis. Nephrol. Dialysis Transplant. 5, 373–374 (2012).
Wang, I.-K. et al. The effect of probiotics on serum levels of cytokine and endotoxin in peritoneal dialysis patients: a randomised, double-blind, placebo-controlled trial. Benef. Microbes 6, 423–430 (2015).
Soleimani, A. et al. Probiotic supplementation in diabetic hemodialysis patients has beneficial metabolic effects. Kidney Int. 91, 435–442 (2017).
Google Scholar
Taki, K., Takayama, F. & Niwa, T. Beneficial effects of bifidobacteria in a gastroresistant seamless capsule on hyperhomocysteinemia in hemodialysis patients. J. Ren. Nutr. 15, 77–80 (2005).
Ikizler, T. A. et al. KDOQI clinical practice guideline for nutrition in CKD: 2020 update. Am. J. Kidney Dis. 76, S1–S107 (2020).
Google Scholar
Stanford, J. et al. High-diversity plant-based diet and gut microbiome, plasma metabolome, and symptoms in adults with CKD. Clin. J. Am. Soc. Nephrol. 20, 619–631 (2025).
Felizardo, R. J. F. et al. Gut microbial metabolite butyrate protects against proteinuric kidney disease through epigenetic- and GPR109a-mediated mechanisms. FASEB J. 33, 11894–11908 (2019).
Google Scholar
Li, Y. J. et al. Dietary fiber protects against diabetic nephropathy through short-chain fatty acid-mediated activation of G protein-coupled receptors GPR43 and GPR109A. J. Am. Soc. Nephrol. 31, 1267–1281 (2020).
Google Scholar
Li, Y. J. et al. Short-chain fatty acids directly exert anti-inflammatory responses in podocytes and tubular epithelial cells exposed to high glucose. Front. Cell Dev. Biol. 11, 1182570 (2023).
Google Scholar
Corte-Iglesias, V. et al. Propionate and butyrate counteract renal damage and progression to chronic kidney disease. Nephrol. Dial. Transpl. 40, 133–150 (2024).
Lobel, L. et al. Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function. Science 369, 1518–1524 (2020).
Google Scholar
Linares, L. et al. Epidemiology and outcomes of multiple antibiotic-resistant bacterial infection in renal transplantation. Transpl. Proc. 39, 2222–2224 (2007).
Google Scholar
Magruder, M. et al. Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nat. Commun. 10, 5521 (2019).
Google Scholar
Shimasaki, T. et al. Increased relative abundance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae within the gut microbiota is associated with risk of bloodstream infection in long-term acute care hospital patients. Clin. Infect. Dis. 68, 2053–2059 (2019).
Taur, Y. et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin. Infect. Dis. 55, 905–914 (2012).
Google Scholar
Ghani, R. et al. Disease prevention not decolonization: a model for fecal microbiota transplantation in patients colonized with multidrug-resistant organisms. Clin. Infect. Dis. 72, 1444–1447 (2021).
Mangalea, M. R. et al. Decolonization and pathogen reduction approaches to prevent antimicrobial resistance and healthcare-associated infections. Emerg. Infect. Dis. 30, 1069 (2024).
Google Scholar
Roman, Y. M. The role of uric acid in human health: insights from the uricase gene. J. Pers. Med. 13, 1409 (2023).
Google Scholar
Krishnan, E. Reduced glomerular function and prevalence of gout: NHANES 2009-10. PLoS ONE 7, e50046 (2012).
Google Scholar
Sorensen, L. B. Role of the intestinal tract in the elimination of uric acid. Arthritis Rheum. 8, 694–706 (1965).
Google Scholar
Vargas-Santos, A. B. & Neogi, T. Management of gout and hyperuricemia in CKD. Am. J. Kidney Dis. 70, 422–439 (2017).
Google Scholar
Liu, Y. et al. A widely distributed gene cluster compensates for uricase loss in hominids. Cell 186, 3400–3413 e20 (2023).
Google Scholar
Kasahara, K. et al. Gut bacterial metabolism contributes to host global purine homeostasis. Cell Host Microbe 31, 1038–1053.e10 (2023).
Google Scholar
Moe, O. W. Kidney stones: pathophysiology and medical management. Lancet 367, 333–344 (2006).
Google Scholar
Filler, G. et al. In focus: perplexing increase of urinary stone disease in children, adolescent and young adult women and its economic impact. Front. Med. 10, 1272900 (2023).
Vo, A. K. et al. Measuring quality of life in patients with kidney stone disease: is it the future in endourology? Curr. Opin. Urol. 34, 91–97 (2024).
Hatch, M. et al. Oxalobacter sp. reduces urinary oxalate excretion by promoting enteric oxalate secretion. Kidney Int. 69, 691–698 (2006).
Google Scholar
Campieri, C. et al. Reduction of oxaluria after an oral course of lactic acid bacteria at high concentration. Kidney Int. 60, 1097–1105 (2001).
Google Scholar
Lieske, J. C. et al. Use of a probiotic to decrease enteric hyperoxaluria. Kidney Int. 68, 1244–1249 (2005).
Google Scholar
Goldfarb, D. S., Modersitzki, F. & Asplin, J. R. A randomized, controlled trial of lactic acid bacteria for idiopathic hyperoxaluria. Clin. J. Am. Soc. Nephrol. 2, 745–749 (2007).
Lieske, J. C. et al. Diet, but not oral probiotics, effectively reduces urinary oxalate excretion and calcium oxalate supersaturation. Kidney Int. 78, 1178–1185 (2010).
Google Scholar
Siener, R. et al. Dietary hyperoxaluria is not reduced by treatment with lactic acid bacteria. J. Transl. Med. 11, 306 (2013).
Google Scholar
Tavasoli, S. et al. Effect of a probiotic supplement containing Lactobacillus acidophilus and Bifidobacterium animalis lactis on urine oxalate in calcium stone formers with hyperoxaluria: a randomized, placebo-controlled, double-blind and in-vitro trial. Urol. J. 19, 179–188 (2021).
Hoppe, B. et al. A randomised phase I/II trial to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria. Pediatr. Nephrol. 32, 781–790 (2017).
Hoppe, B. et al. Efficacy and safety of Oxalobacter formigenes to reduce urinary oxalate in primary hyperoxaluria. Nephrol. Dial. Transpl. 26, 3609–3615 (2011).
Milliner, D., Hoppe, B. & Groothoff, J. A randomised phase II/III study to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria. Urolithiasis 46, 313–323 (2018).
Google Scholar
Mukherjee, S. D. et al. Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria. eLife 14, RP104121 (2025).
Google Scholar
Duranton, F. et al. Normal and pathologic concentrations of uremic toxins. J. Am. Soc. Nephrol. 23, 1258–1270 (2012).
Google Scholar
Waikar, S. S. et al. Association of urinary oxalate excretion with the risk of chronic kidney disease progression. JAMA Intern. Med. 179, 542–551 (2019).
Google Scholar
Ermer, T. et al. Oxalate, inflammasome, and progression of kidney disease. Curr. Opin. Nephrol. Hypertens. 25, 363–371 (2016).
Google Scholar
Pfau, A. et al. High oxalate concentrations correlate with increased risk for sudden cardiac death in dialysis patients. J. Am. Soc. Nephrol. 32, 2375–2385 (2021).
Google Scholar
Choy, W. H. et al. Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease. Urolithiasis 52, 38 (2024).
Google Scholar
Zampini, A. et al. Defining dysbiosis in patients with urolithiasis. Sci. Rep. 9, 5425 (2019).
Google Scholar
Agudelo, J. et al. Cefazolin shifts the kidney microbiota to promote a lithogenic environment. Nat. Commun. 15, 10509 (2024).
Google Scholar
Chesnaye, N. C. et al. Differences in the epidemiology, management and outcomes of kidney disease in men and women. Nat. Rev. Nephrol. 20, 7–20 (2024).
de la Cuesta-Zuluaga, J. et al. Age- and sex-dependent patterns of gut microbial diversity in human adults. mSystems 4, e00261-19 (2019).
Google Scholar
Perez, M. et al. A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects. Gut Microbes 13, 1–19 (2021).
El Houari, A. et al. Development of an in vitro model of human gut microbiota for screening the reciprocal interactions with antibiotics, drugs, and xenobiotics. Front. Microbiol. 13, 828359 (2022).
Google Scholar
Cheng, A. G. et al. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185, 3617–3636.e19 (2022).
Google Scholar
Wang, M. et al. Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome. Cell 186, 2839–2852.e21 (2023).
Google Scholar
Pascal Andreu, V. et al. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat. Biotechnol. 41, 1416–1423 (2023).
Google Scholar
Mei, X. et al. Genetically engineered Lactobacillus paracasei rescues colonic angiotensin converting enzyme 2 (ACE2) and attenuates hypertension in female Ace2 knock out rats. Pharmacol. Res. 196, 106920 (2023).
Google Scholar
Guo, C. J. et al. Depletion of microbiome-derived molecules in the host using clostridium genetics. Science 366, eaav1282 (2019).
Google Scholar
Rubin, B. E. et al. Species- and site-specific genome editing in complex bacterial communities. Nat. Microbiol. 7, 34–47 (2022).
Google Scholar
Brödel, A. K. et al. In situ targeted base editing of bacteria in the mouse gut. Nature 632, 877–884 (2024).
Google Scholar
Ali, N. et al. Advances in CRISPR-Cas systems for gut microbiome. Prog. Mol. Biol. Transl. Sci. 208, 59–81 (2024).
Google Scholar
Kelly, C. R. et al. Fecal microbiota transplant for treatment of Clostridium difficile infection in immunocompromised patients. Am. J. Gastroenterol. 109, 1065–1071 (2014).
Google Scholar
Cheng, Y.-W. et al. Fecal microbiota transplantation for the treatment of recurrent and severe Clostridium difficile infection in solid organ transplant recipients: a multicenter experience. Am. J. Transplant. 19, 501–511 (2019).
Google Scholar
Peery, A. F. et al. AGA clinical practice guideline on fecal microbiota–based therapies for select gastrointestinal diseases. Gastroenterology 166, 409–434 (2024).
Google Scholar
Carlson, P. E. Regulatory considerations for fecal microbiota transplantation products. Cell Host Microbe 27, 173–175 (2020).
Google Scholar
Woodworth, M. H. et al. Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. Sci. Transl. Med. 15, eabo2750 (2023).
Google Scholar
Tang, Q. et al. Current sampling methods for gut microbiota: a call for more precise devices. Front. Cell. Infect. Microbiol. 10, 151 (2020).
Google Scholar
Zhang, X. & Figeys, D. Perspective and guidelines for metaproteomics in microbiome studies. J. Proteome Res. 18, 2370–2380 (2019).
Google Scholar
James, K. R. et al. Distinct microbial and immune niches of the human colon. Nat. Immunol. 21, 343–353 (2020).
Google Scholar
Anandakumar, H. et al. Segmental patterning of microbiota and immune cells in the murine intestinal tract. Gut Microbes 16, 2398126 (2024).
Google Scholar
Shalon, D. et al. Profiling the human intestinal environment under physiological conditions. Nature 617, 581–591 (2023).
Google Scholar
Folz, J. et al. Human metabolome variation along the upper intestinal tract. Nat. Metab. 5, 777–788 (2023).
Google Scholar
Culver, R. N. et al. Improved mouse models of the small intestine microbiota using region-specific sampling from humans. Preprint at bioRxiv (2024).
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