Raman spectroscopy
bacteria
basic science
fungi entombment
geomicrobiology
kidney stone mineralogy
microbiome
nephrolithiasis
super-resolution autofluorescence (SRAF) microscopy
urolithiasis
Journal
Kidney360
ISSN: 2641-7650
Titre abrégé: Kidney360
Pays: United States
ID NLM: 101766381
Informations de publication
Date de publication:
25 02 2021
25 02 2021
Historique:
received:
23
11
2020
accepted:
23
12
2020
entrez:
4
4
2022
pubmed:
23
12
2020
medline:
8
4
2022
Statut:
epublish
Résumé
Human kidney stones form Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including These results indicate a microbiome is entombed during
Sections du résumé
Background
Human kidney stones form
Methods
Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions.
Results
Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including
Conclusions
These results indicate a microbiome is entombed during
Identifiants
pubmed: 35373025
doi: 10.34067/KID.0006942020
pii: 02200512-202102000-00013
pmc: PMC8740987
doi:
Substances chimiques
Calcium Phosphates
0
RNA, Ribosomal, 16S
0
Calcium Oxalate
2612HC57YE
Struvite
AW3EJL1462
calcium phosphate, dibasic, dihydrate
O7TSZ97GEP
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
298-311Informations de copyright
Copyright © 2021 by the American Society of Nephrology.
Déclaration de conflit d'intérêts
A. Krambeck reports consultancy agreements with Boston Scientific, Lumenis, Sonomotion, and Virtuoso; receiving research funding from Boston Scientific, Lumenis; receiving honoraria from Boston Scientific, Lumenis, Sonomotion, and Virtuoso; reports having patents and inventions b7h1 and Survivin as a marker for Renal Cell Carcinoma; and reports being a scientific advisor or member of Boston Scientific, Sonomotion, and Virtuoso. B. Fouke reports receiving research funding from Dornier MedTech. D. Lange reports having consultancy agreements with AdvaTec, BD/Bard, Boston Scientific, Cook Medical, and Kisolite; having an ownership interest in Kisolite Corp; reports receiving research funding from AdvaTec, BD/Bard, Boston Scientific, and Cook Medical; and reports scientific advisor or membership of Kisolite Corp. J. Lieske reports having consultancy agreements with Alnylam, Allena, American Board of Internal Medicine, Dicerna, Orfan, OxThera, Retrophin, and Siemens; reports receiving research funding from Allena, Alnylam, Dicerna, OxThera, Retrophin, and Siemens; reports receiving honoraria from Alnylam, Allena, American Board of Internal Medicine, Dicerna, Retrophin, Novobiome, Orfan, OxThera, and Synlogic; scientific advisor or membership of American Board of Internal Medicine, Hyperoxaluria Foundation, Kidney International, and Oxalosis. M. Rivera reports consultancy agreements with Boston Scientific, Cook Medical and Lumenis. M. Romero reports scientific advisor or membership of Kidney360 - Associate Editor, American Journal of Physiology-Renal Physiology, Hyperoxaluria Foundation, Oxalosis, National Institute of Diabetes and Digestive and Kidney Diseases study sections, ad hoc. N. Chia reports receiving research funding from Archer Daniels Midland. T. Large reports having consultancy agreements with Boston Scientific and Lumenis. Y. Dong reports being a scientific advisor or member of Frontiers in Microbiology. All remaining authors have nothing to disclose. All remaining authors have nothing to disclose.
Références
GBD Chronic Kidney Disease Collaboration: Global, regional, and national burden of chronic kidney disease, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017. Lancet 395: 709–733, 2020 https://doi.org/10.1016/S0140-6736(20)30045-3
doi: 10.1016/S0140-6736(20)30045-3
Sivaguru M, Lieske JC, Krambeck AE, Fouke BW: GeoBioMed sheds new light on human kidney stone crystallization and dissolution. Nat Rev Urol 17: 1–2, 2020 https://doi.org/10.1038/s41585-019-0256-5
doi: 10.1038/s41585-019-0256-5
Sivaguru M, Saw JJ, Williams JC Jr, Lieske JC, Krambeck AE, Romero MF, Chia N, Schwaderer AL, Alcalde RE, Bruce WJ, Wildman DE, Fried GA, Werth CJ, Reeder RJ, Yau PM, Sanford RA, Fouke BW: Geobiology reveals how human kidney stones dissolve in vivo . Sci Rep 8: 13731, 2018 https://doi.org/10.1038/s41598-018-31890-9
doi: 10.1038/s41598-018-31890-9
Basavaraj DR, Biyani CS, Browning AJ, Cartledge JJ: The role of urinary kidney stone inhibitors and promoters in the pathogenesis of calcium containing renal stones. EAU-EBU Update Ser 5: 126–136, 2007 https://doi.org/10.1016/j.eeus.2007.03.002
doi: 10.1016/j.eeus.2007.03.002
Schwaderer AL, Wolfe AJ: The association between bacteria and urinary stones. Ann Transl Med 5: 32, 2017 https://doi.org/10.21037/atm.2016.11.73
doi: 10.21037/atm.2016.11.73
Fouke BW: Hot-spring systems geobiology: Abiotic and biotic influences on travertine formation at Mammoth Hot Springs, Yellowstone National Park, USA. Sedimentology 58: 170–219, 2011 https://doi.org/10.1111/j.1365-3091.2010.01209.x
doi: 10.1111/j.1365-3091.2010.01209.x
Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW: Physiology, metabolism, and fossilization of hot-spring filamentous microbial mats. Astrobiology 19: 1442–1458, 2019 https://doi.org/10.1089/ast.2018.1965
doi: 10.1089/ast.2018.1965
Warscheid T, Braams J: Biodeterioration of stone: A review. Int Biodeterior Biodegradation 46: 343–368, 2000 https://doi.org/10.1016/S0964-8305(00)00109-8
doi: 10.1016/S0964-8305(00)00109-8
de Cógáin MR, Lieske JC, Vrtiska TJ, Tosh PK, Krambeck AE: Secondarily infected nonstruvite urolithiasis: A prospective evaluation. Urology 84: 1295–1300, 2014 https://doi.org/10.1016/j.urology.2014.08.007
doi: 10.1016/j.urology.2014.08.007
Barr-Beare E, Saxena V, Hilt EE, Thomas-White K, Schober M, Li B, Becknell B, Hains DS, Wolfe AJ, Schwaderer AL: The interaction between enterobacteriaceae and calcium oxalate deposits. PLoS One 10: e0139575, 2015 https://doi.org/10.1371/journal.pone.0139575
doi: 10.1371/journal.pone.0139575
Rose E, Zampini AM, Nguyen AH, Monga M, Miller AW: MP24-05 the urine and stone microbiome in kidney stone patients. J Urol 199[4S]: e291, 2018 https://doi.org/10.1016/j.juro.2018.02.758
doi: 10.1016/j.juro.2018.02.758
Dornbier RA, Bajic P, Van Kuiken M, Jardaneh A, Lin H, Gao X, Knudsen B, Dong Q, Wolfe AJ, Schwaderer AL: The microbiome of calcium-based urinary stones. Urolithiasis 48: 191–199, 2020 https://doi.org/10.1007/s00240-019-01146-w
doi: 10.1007/s00240-019-01146-w
Miller AW, Choy D, Penniston KL, Lange D: Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis. Kidney Int 96: 180–188, 2019 https://doi.org/10.1016/j.kint.2019.02.012
doi: 10.1016/j.kint.2019.02.012
Flannigan R, Choy WH, Chew B, Lange D: Renal struvite stones--pathogenesis, microbiology, and management strategies. Nat Rev Urol 11: 333–341, 2014 https://doi.org/10.1038/nrurol.2014.99
doi: 10.1038/nrurol.2014.99
McMurdie PJ, Holmes S: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8: e61217, 2013 https://doi.org/10.1371/journal.pone.0061217
doi: 10.1371/journal.pone.0061217
R Core Team: R: A Language and Environment for Statistical Computing, Vienna, Austria, R Foundation for Statistical Computing, 2013
Mehta M, Goldfarb DS, Nazzal L: The role of the microbiome in kidney stone formation. Int J Surg 36: 607–612, 2016 https://doi.org/10.1016/j.ijsu.2016.11.024
doi: 10.1016/j.ijsu.2016.11.024
Devaux CA, Raoult D: The microbiological memory, an epigenetic regulator governing the balance between good health and metabolic disorders. Front Microbiol 9: 1379, 2018 https://doi.org/10.3389/fmicb.2018.01379
doi: 10.3389/fmicb.2018.01379
Ticinesi A, Nouvenne A, Chiussi G, Castaldo G, Guerra A, Meschi T: Calcium oxalate nephrolithiasis and gut microbiota: Not just a gut-kidney axis. A nutritional perspective. Nutrients 12: 548, 2020 https://doi.org/10.3390/nu12020548
doi: 10.3390/nu12020548
Zampini A, Nguyen AH, Rose E, Monga M, Miller AW: Defining dysbiosis in patients with urolithiasis. Sci Rep 9: 5425, 2019 https://doi.org/10.1038/s41598-019-41977-6
doi: 10.1038/s41598-019-41977-6
Prywer J, Torzewska A, Płociński T: Unique surface and internal structure of struvite crystals formed by Proteus mirabilis. Urol Res 40: 699–707, 2012 https://doi.org/10.1007/s00240-012-0501-3
doi: 10.1007/s00240-012-0501-3
Tasian G, Miller A, Lange D: Antibiotics and kidney stones: Perturbation of the gut-kidney axis. Am J Kidney Dis 74: 724–726, 2019 https://doi.org/10.1053/j.ajkd.2019.07.021
doi: 10.1053/j.ajkd.2019.07.021
Allison MJ, Dawson KA, Mayberry WR, Foss JG: Oxalobacter formigenes gen. nov., sp. nov.: Oxalate-degrading anaerobes that inhabit the gastrointestinal tract. Arch Microbiol 141: 1–7, 1985 https://doi.org/10.1007/BF00446731
doi: 10.1007/BF00446731
Kaufman DW, Kelly JP, Curhan GC, Anderson TE, Dretler SP, Preminger GM, Cave DR: Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones. J Am Soc Nephrol 19: 1197–1203, 2008 https://doi.org/10.1681/ASN.2007101058
doi: 10.1681/ASN.2007101058
Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF, Guo JN: Profiling the urinary microbiome in men with calcium-based kidney stones. BMC Microbiol 20: 41, 2020 https://doi.org/10.1186/s12866-020-01734-6
doi: 10.1186/s12866-020-01734-6
Peck AB, Canales BK, Nguyen CQ: Oxalate-degrading microorganisms or oxalate-degrading enzymes: Which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease? Urolithiasis 44: 45–50, 2016 https://doi.org/10.1007/s00240-015-0845-6
doi: 10.1007/s00240-015-0845-6
Lange D: Editorial Comment on: Calcium Oxalate Urolithiasis: A Case of Missing Microbes? by Batagello et al. J Endourol 32: 1006, 2018 https://doi.org/10.1089/end.2018.0606
doi: 10.1089/end.2018.0606
Lieske JC, Goldfarb DS, De Simone C, Regnier C: Use of a probiotic to decrease enteric hyperoxaluria. Kidney Int 68: 1244–1249, 2005 https://doi.org/10.1111/j.1523-1755.2005.00520.x
doi: 10.1111/j.1523-1755.2005.00520.x
Siener R, Netzer L, Hesse A: Determinants of brushite stone formation: A case-control study. PLoS One 8: e78996, 2013 https://doi.org/10.1371/journal.pone.0078996
doi: 10.1371/journal.pone.0078996
Golechha S, Solanki A: Bacteriology and chemical composition of renal calculi accompanying urinary tract infection. Indian J Urol 17: 111–117, 2001
Pluznick JL: The gut microbiota in kidney disease. Science 369: 1426–1427, 2020 https://doi.org/10.1126/science.abd8344
doi: 10.1126/science.abd8344
Kandianis MT, Fouke BW, Johnson RW, Veysey J, Inskeep WP: Microbial biomass: A catalyst for CaCO3 precipitation in advection-dominated transport regimes. Geol Soc Am Bull 120: 442–450, 2008 https://doi.org/10.1130/B26188.1
doi: 10.1130/B26188.1
Seiffert F, Bandow N, Kalbe U, Milke R, Gorbushina AA: Laboratory tools to quantify biogenic dissolution of rocks and minerals: A model rock biofilm growing in percolation columns. Front Earth Sci 4: 31, 2016 https://doi.org/10.3389/feart.2016.00031
doi: 10.3389/feart.2016.00031
Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA: Brock Biology of Microorganisms, 15th Ed., New York, Pearson, 2017
Sivaguru M, Fouke KW, Todorov L, Kingsford MJ, Fouke KE, Trop JM, Fouke BW: Correction factors for δ 18 O-derived global sea surface temperature reconstructions from diagenetically altered intervals of coral skeletal density banding. Front Mar Sci 6, 2019 https://doi.org/10.3389/fmars.2019.00306
doi: 10.3389/fmars.2019.00306
Khan SR, Atmani F, Glenton P, Hou Z, Talham DR, Khurshid M: Lipids and membranes in the organic matrix of urinary calcific crystals and stones. Calcif Tissue Int 59: 357–365, 1996 https://doi.org/10.1007/s002239900140
doi: 10.1007/s002239900140
Verkoelen CF: Crystal retention in renal stone disease: A crucial role for the glycosaminoglycan hyaluronan? J Am Soc Nephrol 17: 1673–1687, 2006 https://doi.org/10.1681/ASN.2006010088
doi: 10.1681/ASN.2006010088
Canales BK, Anderson L, Higgins L, Ensrud-Bowlin K, Roberts KP, Wu B, Kim IW, Monga M: Proteome of human calcium kidney stones. Urology 76: 1017.e13–1017.e20, 2010 https://doi.org/10.1016/j.urology.2010.05.005
doi: 10.1016/j.urology.2010.05.005
Skinner CWHIn: The Scientific Basis of Orthopaedics, edited by Albright J. A., Brand R., Norwalk, CT, Appleton and Lange, 1987, pp 198–212
Liu X, Li J, Xiang L, Sun J, Zheng G, Zhang G, Wang H, Xie L, Zhang R: The role of matrix proteins in the control of nacreous layer deposition during pearl formation. Proc Biol Sci 279: 1000–1007, 2012 https://doi.org/10.1098/rspb.2011.1661
doi: 10.1098/rspb.2011.1661
Addadi L, Weiner S: Biomineralization: Mineral formation by organisms. Phys Scr 89: 098003, 2014 https://doi.org/10.1088/0031-8949/89/9/098003
doi: 10.1088/0031-8949/89/9/098003
Pernice M, Raina JB, Rädecker N, Cárdenas A, Pogoreutz C, Voolstra CR: Down to the bone: The role of overlooked endolithic microbiomes in reef coral health. ISME J 14: 325–334, 2020 https://doi.org/10.1038/s41396-019-0548-z
doi: 10.1038/s41396-019-0548-z
Wesson JA, Worcester EM, Wiessner JH, Mandel NS, Kleinman JG: Control of calcium oxalate crystal structure and cell adherence by urinary macromolecules. Kidney Int 53: 952–957, 1998 https://doi.org/10.1111/j.1523-1755.1998.00839.x
doi: 10.1111/j.1523-1755.1998.00839.x
Gadd GM, Bahri-Esfahani J, Li Q, Rhee YJ, Wei Z, Fomina M, Liang X: Oxalate production by fungi: Significance in geomycology, biodeterioration and bioremediation. Fungal Biol Rev 28: 36–55, 2014 https://doi.org/10.1016/j.fbr.2014.05.001
doi: 10.1016/j.fbr.2014.05.001
Sturm VE, Frank-Kamenetskaya O, Vlasov D, Zelenskaya M, Sazanova K, Rusakov A, Kniep R: Crystallization of calcium oxalate hydrates by interaction of calcite marble with fungus Aspergillus niger. Am Mineral 100: 2559–2565, 2015 https://doi.org/10.2138/am-2015-5104
doi: 10.2138/am-2015-5104
Kuliasha CA, Rodriguez D, Lovett A, Gower LB: In situ flow cell platform for examining calcium oxalate and calcium phosphate crystallization on films of basement membrane extract in the presence of urinary ‘inhibitors’. CrystEngComm 22: 1448–1458, 2020 https://doi.org/10.1039/C9CE01587F
doi: 10.1039/C9CE01587F
Al KF: Characterizing the role of the microbiome in kidney stone disease. Doctor of Philosophy Thesis, University of Western Ontario, 2020. Available at: https://ir.lib.uwo.ca/etd/7122