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Cited by 88Gut microbiota and healthKidney Stones and Urolithiasis TreatmentsMicrobial metabolism and enzyme function

Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist

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Daniel, Steven L., Moradi, Luke, Paiste, Henry, Wood, Kyle D., Assimos, Dean G., Holmes, Ross P., Nazzal, Lama, Hatch, Marguerite +1 more·2021·Applied and Environmental Microbiology
DOI 10.1128/aem.00544-21PMC PMC8388816
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Abstract

Oxalobacter formigenes , a unique anaerobic bacterium that relies solely on oxalate for growth, is a key oxalate-degrading bacterium in the mammalian intestinal tract. Degradation of oxalate in the gut by O. formigenes plays a critical role in preventing renal toxicity in animals that feed on oxalate-rich plants.

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  • There are many key functions that are only carried out by a relatively small number of microbiota species, with examples including oxalate and resistant-starch degradation.

    “there are many key functions that are only carried out by a relatively small number of microbiota species. Examples include oxalate 31 and resistant-starch 32 degradation.”

    From Human microbiome myths and misconceptions (2023) · cites this paper as [31]

    The Introduction identifies O. formigenes as an oxalate-degrading specialist and says it dominates oxalate degradation transcriptionally in healthy adults. It also describes diverse bacteria capable of degrading oxalate, so it does not establish that only a relatively small number of species carry out the function. Citation 31 is attached to oxalate degradation; resistant-starch degradation has a separate citation. (LLM, conf=0.82)

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References 118 · Cited by 88

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  1. [1]Morris M, Garcia-Rivera J. 1955. The destruction of oxalates by the rumen contents of cows. J Dairy Sci 38:1169. 10.3168/jds.S0022-0302(55)95091-8. [DOI] [Google Scholar] · DOI
  2. [2]Talapatra S, Ray S, Sen K. 1948. Calcium assimilation in ruminants on oxalate-rich diet. J Agric Sci 38:163–173. 10.1017/S0021859600005426. [DOI] [Google Scholar] · DOI
  3. [3]Hodgkinson A. 1977. Oxalic acid in biology and medicine. Academic Press, New York, NY. [Google Scholar]
  4. [4]James LF, Butcher JE. 1972. Halogeton poisoning of sheep: effect of high level oxalate intake. J Anim Sci 35:1233–1238. 10.2527/jas1972.3561233x. [DOI] [PubMed] [Google Scholar] · DOI
  5. [5]James LF, Street JC, Butcher JE. 1967. In vitro degradation of oxalate and of cellulose by rumen ingesta from sheep fed Halogeton glomeratus. J Anim Sci 26:1438–1444. 10.2527/jas1967.2661438x. [DOI] [PubMed] [Google Scholar] · DOI
  6. [6]James LF, Cronin EH. 1974. Management practices to minimize death losses of sheep grazing halogeton-infested range. J Range Sci 27:424–426. 10.2307/3896714. [DOI] [Google Scholar] · DOI
  7. [7]Dodson M. 1959. Oxalate ingestion studies in sheep. Aust Vet J 35:225–233. [Google Scholar]
  8. [8]Allison MJ, Littledike ET, James LF. 1977. Changes in ruminal oxalate degradation rates associated with adaptation to oxalate ingestion. J Anim Sci 45:1173–1179. 10.2527/jas1977.4551173x. [DOI] [PubMed] [Google Scholar] · DOI
  9. [9]Daniel SL, Cook HM, Hartman PA, Allison MJ. 1989. Enumeration of anaerobic oxalate-degrading bacteria in the ruminal contents of sheep. FEMS Microbiol Lett 62:329–334. 10.1111/j.1574-6968.1989.tb03387.x. [DOI] [Google Scholar] · DOI
  10. [10]Dawson KA, Allison MJ, Hartman PA. 1980. Isolation and some characteristics of anaerobic oxalate-degrading bacteria from the rumen. Appl Environ Microbiol 40:833–839. 10.1128/aem.40.4.833-839.1980. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  11. [11]Allison MJ, Dawson KA, Mayberry WR, Foss JG. 1985. Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract. Arch Microbiol 141:1–7. 10.1007/BF00446731. [DOI] [PubMed] [Google Scholar] · DOI
  12. [12]Hatch M, Freel RW. 2005. Intestinal transport of an obdurate anion: oxalate. Urol Res 33:1–16. 10.1007/s00240-004-0445-3. [DOI] [PubMed] [Google Scholar] · DOI
  13. [13]Knight J, Deora R, Assimos DG, Holmes RP. 2013. The genetic composition of Oxalobacter formigenes and its relationship to colonization and calcium oxalate stone disease. Urolithiasis 41:187–196. 10.1007/s00240-013-0566-7. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  14. [14]Whittamore JM, Hatch M. 2017. The role of intestinal oxalate transport in hyperoxaluria and the formation of kidney stones in animals and man. Urolithiasis 45:89–108. 10.1007/s00240-016-0952-z. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  15. [15]Jensen NS, Allison MJ. 1994. Studies on the diversity among anaerobic oxalate-degrading bacteria now in the species Oxalobacter formigenes. In94th general meeting of the American Society for Microbiology. American Society for Microbiology, Washington, D.C. [Google Scholar]
  16. [16]Allison MJ, MacGregor BJ, Sharp R, Stahl DA. 2015. Oxalobacter, p 1–8. In Whitman WB (ed), Bergey's manual of systematics of Archaea and Bacteria. John Wiley & Sons, Inc. [Google Scholar]
  17. [17]Sidhu H, Allison M, Peck AB. 1997. Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers. J Clin Microbiol 35:350–353. 10.1128/jcm.35.2.350-353.1997. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  18. [18]Daniel SL, Hartman PA, Allison MJ. 1987. Microbial degradation of oxalate in the gastrointestinal tracts of rats. Appl Environ Microbiol 53:1793–1797. 10.1128/aem.53.8.1793-1797.1987. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  19. [19]Dawson KA. 1979. Enrichment, isolation and characterization of anaerobic oxalate-degrading bacteria from the rumen. PhD thesis. Iowa State University, Ames, IA. [Google Scholar]
  20. [20]Cornick NA, Allison MJ. 1996. Assimilation of oxalate, acetate, and CO2 by Oxalobacter formigenes. Can J Microbiol 42:1081–1086. 10.1139/m96-138. [DOI] [PubMed] [Google Scholar] · DOI
  21. [21]Cornick NA, Allison MJ. 1996. Anabolic incorporation of oxalate by Oxalobacter formigenes. Appl Environ Microbiol 62:3011–3013. 10.1128/aem.62.8.3011-3013.1996. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  22. [22]Cornick NA, Yan B, Bank S, Allison MJ. 1996. Biosynthesis of amino acids by Oxalobacter formigenes: analysis using 13C-NMR. Can J Microbiol 42:1219–1224. 10.1139/m96-157. [DOI] [Google Scholar] · DOI
  23. [23]Anantharam V, Allison MJ, Maloney PC. 1989. Oxalate:formate exchange. The basis for energy coupling in Oxalobacter. J Biol Chem 264:7244–7250. 10.1016/S0021-9258(18)83227-6. [DOI] [PubMed] [Google Scholar] · DOI
  24. [24]Kuhner CH, Hartman PA, Allison MJ. 1996. Generation of a proton motive force by the anaerobic oxalate-degrading bacterium Oxalobacter formigenes. Appl Environ Microbiol 62:2494–2500. 10.1128/aem.62.7.2494-2500.1996. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  25. [25]Bryant M. 1972. Commentary on the Hungate technique for culture of anaerobic bacteria. Am J Clin Nutr 25:1324–1328. 10.1093/ajcn/25.12.1324. [DOI] [PubMed] [Google Scholar] · DOI
  26. [26]Holdeman L, Cato E, Moore W. 1977. Anaerobe laboratory manual, VPI Anaerobe Laboratory, Virginia Polytechnic Institute and State University, Blacksburg, Virginia. [Google Scholar]
  27. [27]Hungate R. 1969. Chapter IV: a roll tube method for cultivation of strict anaerobes, p 117–132, Methods in microbiology, vol 3. Elsevier, Amsterdam, Netherlands. [Google Scholar]
  28. [28]Allison MJ, Daniel SL, Cornick NA. 1995. Oxalate degrading bacteria, p 131–168. In Khan SR (ed), Calcium oxalate in biological systems. CRC Press, New York, NY. [Google Scholar]
  29. [29]Ellis ML, Dowell AE, Li X, Knight J. 2016. Probiotic properties of Oxalobacter formigenes: an in vitro examination. Arch Microbiol 198:1019–1026. 10.1007/s00203-016-1272-y. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  30. [30]Sun NY, Gao Y, Yu HJ. 2019. Genome sequence of Oxalobacter formigenes strain SSYG-15. Microbiol Resour Announc 8:e01059-19. 10.1128/MRA.01059-19. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  31. [31]Hatch M, Allison MJ, Yu F, Farmerie W. 2017. Genome sequence of Oxalobacter formigenes strain OXCC13. Genome Announc 5:e00534-17. 10.1128/genomeA.00534-17. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  32. [32]Hatch M, Allison MJ, Yu F, Farmerie W. 2017. Genome sequence of Oxalobacter formigenes strain HC-1. Genome Announc 5:e00533-17. 10.1128/genomeA.00533-17. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  33. [33]Ellis ME, Mobley JA, Holmes RP, Knight J. 2016. Proteome dynamics of the specialist oxalate degrader Oxalobacter formigenes. J Proteomics Bioinform 9:19–24. 10.4172/jpb.1000384. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  34. [34]Reister M, Hoffmeier K, Krezdorn N, Rotter B, Liang C, Rund S, Dandekar T, Sonnenborn U, Oelschlaeger TA. 2014. Complete genome sequence of the Gram-negative probiotic Escherichia coli strain Nissle 1917. J Biotechnol 187:106–107. 10.1016/j.jbiotec.2014.07.442. [DOI] [PubMed] [Google Scholar] · DOI
  35. [35]Jacobi CA, Malfertheiner P. 2011. Escherichia coli Nissle 1917 (Mutaflor): new insights into an old probiotic bacterium. Dig Dis 29:600–607. 10.1159/000333307. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  36. [36]Gao NL, Chen J, Wang T, Lercher MJ, Chen W-H. 2019. Prokaryotic genome expansion is facilitated by phages and plasmids but impaired by CRISPR. Front Microbiol 10:2254. 10.3389/fmicb.2019.02254. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  37. [37]Long M, Betrán E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nat Rev Genet 4:865–875. 10.1038/nrg1204. [DOI] [PubMed] [Google Scholar] · DOI · Paper page
  38. [38]Ou Y, McInerney JO. 2019. Eukaryote genes are more likely than prokaryote genes to be composites. Genes 10:648. 10.3390/genes10090648. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  39. [39]Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. 2019. Microbial genome analysis: the COG approach. Brief Bioinform 20:1063–1070. 10.1093/bib/bbx117. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  40. [40]Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV. 2021. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 49:D274–D281. 10.1093/nar/gkaa1018. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  41. [41]Chamberlain CA, Hatch M, Garrett TJ. 2020. Oxalobacter formigenes produces metabolites and lipids undetectable in oxalotrophic Bifidobacterium animalis. Metabolomics 16:122. 10.1007/s11306-020-01747-2. [DOI] [PubMed] [Google Scholar] · DOI
  42. [42]Chamberlain CA, Hatch M, Garrett TJ. 2019. Metabolomic and lipidomic characterization of Oxalobacter formigenes strains HC1 and OxWR by UHPLC-HRMS. Anal Bioanal Chem 411:4807–4818. 10.1007/s00216-019-01639-y. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  43. [43]Kumar R, Mukherjee M, Bhandari M, Kumar A, Sidhu H, Mittal RD. 2002. Role of Oxalobacter formigenes in calcium oxalate stone disease: a study from North India. Eur Urol 41:318–322. 10.1016/S0302-2838(02)00040-4. [DOI] [PubMed] [Google Scholar] · DOI
  44. [44]Kwak C, Jeong BC, Kim HK, Kim EC, Chox MS, Kim HH. 2003. Molecular epidemiology of fecal Oxalobacter formigenes in healthy adults living in Seoul, Korea. J Endourol 17:239–243. 10.1089/089277903765444384. [DOI] [PubMed] [Google Scholar] · DOI
  45. [45]Kodama T, Mikami K, Akakura K, Takei K, Naya Y, Ueda T, Ito H. 2003. Detection of Oxalobacter formigenes in human feces and study of related genes in a new oxalate-degrading bacterium (in Japanese). Hinyokika Kiyo 49:371–376. [PubMed] [Google Scholar]
  46. [46]Barnett C, Nazzal L, Goldfarb DS, Blaser MJ. 2016. The presence of Oxalobacter formigenes in the microbiome of healthy young adults. J Urol 195:499–506. 10.1016/j.juro.2015.08.070. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  47. [47]Kelly JP, Curhan GC, Cave DR, Anderson TE, Kaufman DW. 2011. Factors related to colonization with Oxalobacter formigenes in U.S. adults. J Endourol 25:673–679. 10.1089/end.2010.0462. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  48. [48]PeBenito A, Nazzal L, Wang C, Li H, Jay M, Noya-Alarcon O, Contreras M, Lander O, Leach J, Dominguez-Bello MG, Blaser MJ. 2019. Comparative prevalence of Oxalobacter formigenes in three human populations. Sci Rep 9:574. 10.1038/s41598-018-36670-z. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  49. [50]Blaser MJ. 2018. Our missing microbes: short-term antibiotic courses have long-term consequences. Cleve Clin J Med 85:928–930. 10.3949/ccjm.85gr.18005. [DOI] [PubMed] [Google Scholar] · DOI
  50. [51]Liu M, Koh H, Kurtz ZD, Battaglia T, PeBenito A, Li H, Nazzal L, Blaser MJ. 2017. Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project. Microbiome 5:108. 10.1186/s40168-017-0316-0. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  51. [52]Sidhu H, Enatska L, Ogden S, Williams WN, Allison MJ, Peck AB. 1997. Evaluating children in the Ukraine for colonization with the intestinal bacterium Oxalobacter formigenes, using a polymerase chain reaction-based detection system. Mol Diagn 2:89–97. 10.1016/S1084-8592(97)80015-X. [DOI] [PubMed] [Google Scholar] · DOI
  52. [53]Cornelius JG, Peck AB. 2004. Colonization of the neonatal rat intestinal tract from environmental exposure to the anaerobic bacterium Oxalobacter formigenes. J Med Microbiol 53:249–254. 10.1099/jmm.0.05418-0. [DOI] [PubMed] [Google Scholar] · DOI
  53. [54]Hatch M. 2017. Gut microbiota and oxalate homeostasis. Ann Transl Med 5:36. 10.21037/atm.2016.12.70. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  54. [55]Li X, Ellis ML, Dowell AE, Kumar R, Morrow CD, Schoeb TR, Knight J. 2016. Response of germ-free mice to colonization with Oxalobacter formigenes and altered Schaedler flora. Appl Environ Microbiol 82:6952–6960. 10.1128/AEM.02381-16. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  55. [56]Jiang J, Knight J, Easter LH, Neiberg R, Holmes RP, Assimos DG. 2011. Impact of dietary calcium and oxalate, and Oxalobacter formigenes colonization on urinary oxalate excretion. J Urol 186:135–139. 10.1016/j.juro.2011.03.006. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  56. [57]Li X, Ellis ML, Knight J. 2015. Oxalobacter formigenes colonization and oxalate dynamics in a mouse model. Appl Environ Microbiol 81:5048–5054. 10.1128/AEM.01313-15. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  57. [58]Hatch M, Cornelius J, Allison M, Sidhu H, Peck A, Freel RW. 2006. Oxalobacter sp. reduces urinary oxalate excretion by promoting enteric oxalate secretion. Kidney Int 69:691–698. 10.1038/sj.ki.5000162. [DOI] [PubMed] [Google Scholar] · DOI
  58. [59]Canales BK, Hatch M. 2014. Kidney stone incidence and metabolic urinary changes after modern bariatric surgery: review of clinical studies, experimental models, and prevention strategies. Surg Obes Relat Dis 10:734–742. 10.1016/j.soard.2014.03.026. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  59. [60]Balk EM, Adam GP, Langberg VN, Earley A, Clark P, Ebeling PR, Mithal A, Rizzoli R, Zerbini CAF, Pierroz DD, Dawson-Hughes B, International Osteoporosis Foundation Calcium Steering Committee. 2017. Global dietary calcium intake among adults: a systematic review. Osteoporos Int 28:3315–3324. 10.1007/s00198-017-4230-x. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  60. [61]Joshi S, Goldfarb DS. 2019. The use of antibiotics and risk of kidney stones. Curr Opin Nephrol Hypertens 28:311–315. 10.1097/MNH.0000000000000510. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  61. [62]Mittal RD, Kumar R, Bid HK, Mittal B. 2005. Effect of antibiotics on Oxalobacter formigenes colonization of human gastrointestinal tract. J Endourol 19:102–106. 10.1089/end.2005.19.102. [DOI] [PubMed] [Google Scholar] · DOI
  62. [63]Tasian GE, Jemielita T, Goldfarb DS, Copelovitch L, Gerber JS, Wu Q, Denburg MR. 2018. Oral antibiotic exposure and kidney stone disease. JASN 29:1731–1740. 10.1681/ASN.2017111213. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  63. [64]Lange JN, Wood KD, Wong H, Otto R, Mufarrij PW, Knight J, Akpinar H, Holmes RP, Assimos DG. 2012. Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics. Urology 79:1286–1289. 10.1016/j.urology.2011.11.017. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  64. [65]Sidhu H, Hoppe B, Hesse A, Tenbrock K, Bromme S, Rietschel E, Peck AB. 1998. Absence of Oxalobacter formigenes in cystic fibrosis patients: a risk factor for hyperoxaluria. Lancet 352:1026–1029. 10.1016/S0140-6736(98)03038-4. [DOI] [PubMed] [Google Scholar] · DOI
  65. [66]Sidhu H, Schmidt Cornelius JG, Thamiselvam S, Khan SR, Hesse A, Peck AB. 1999. Direct correlation between hyperoxaluria/oxalate stone disease and the absence of the gastrointestinal tract dwelling bacterium Oxalobacter formigenes: possible prevention by gut recolonization or enzyme replacement therapy. J Am Soc Nephrol 10:S334–S340. [PubMed] [Google Scholar]
  66. [67]Siener R, Ebert D, Hesse A. 2001. Urinary oxalate excretion in female calcium oxalate stone formers with and without a history of recurrent urinary tract infections. Urol Res 29:245–248. 10.1007/s002400100198. [DOI] [PubMed] [Google Scholar] · DOI
  67. [68]Kharlamb V, Schelker J, Francois F, Jiang J, Holmes RP, Goldfarb DS. 2011. Oral antibiotic treatment of Helicobacter pylori leads to persistently reduced intestinal colonization rates with Oxalobacter formigenes. J Endourol 25:1781–1785. 10.1089/end.2011.0243. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  68. [69]McDonald JAK. 2017. In vitro models of the human microbiota and microbiome. Emerg Top Life Sci 1:373–384. 10.1042/ETLS20170045. [DOI] [PubMed] [Google Scholar] · DOI
  69. [70]Dawson KA, Allison MJ, Hartman PA. 1980. Characteristics of anaerobic oxalate-degrading enrichment cultures from the rumen. Appl Environ Microbiol 40:840–846. 10.1128/aem.40.4.840-846.1980. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  70. [71]Hatch M, Gjymishka A, Salido EC, Allison MJ, Freel RW. 2011. Enteric oxalate elimination is induced and oxalate is normalized in a mouse model of primary hyperoxaluria following intestinal colonization with Oxalobacter. Am J Physiol Gastrointest Liver Physiol 300:G461–G469. 10.1152/ajpgi.00434.2010. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  71. [72]Hatch M. 2020. Induction of enteric oxalate secretion by Oxalobacter formigenes in mice does not require the presence of either apical oxalate transport proteins Slc26A3 or Slc26A6. Urolithiasis 48:1–8. 10.1007/s00240-019-01144-y. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  72. [73]Robertson WG, Peacock M, Heyburn PJ, Hanes FA. 1980. Epidemiological risk factors in calcium stone disease. Scand J Urol Nephrol Suppl 53:15–30. [PubMed] [Google Scholar]
  73. [74]Batislam E, Yilmaz E, Yuvanc E, Kisa O, Kisa U. 2012. Quantitative analysis of colonization with real-time PCR to identify the role of Oxalobacter formigenes in calcium oxalate urolithiasis. Urol Res 40:455–460. 10.1007/s00240-011-0449-8. [DOI] [PubMed] [Google Scholar] · DOI
  74. [75]Troxel SA, Sidhu H, Kaul P, Low RK. 2003. Intestinal Oxalobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate. J Endourol 17:173–176. 10.1089/089277903321618743. [DOI] [PubMed] [Google Scholar] · DOI
  75. [76]Siener R, Bangen U, Sidhu H, Honow R, von Unruh G, Hesse A. 2013. The role of Oxalobacter formigenes colonization in calcium oxalate stone disease. Kidney Int 83:1144–1149. 10.1038/ki.2013.104. [DOI] [PubMed] [Google Scholar] · DOI
  76. [77]Han JZ, Zhang X, Li JG, Zhang YS. 1995. The relationship of Oxalobacter formigenes and calcium oxalate calculi. J Tongji Med Univ 15:249–252. 10.1007/BF02887957. [DOI] [PubMed] [Google Scholar] · DOI
  77. [78]Kaufman DW, Kelly JP, Curhan GC, Anderson TE, Dretler SP, Preminger GM, Cave DR. 2008. Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones. J Am Soc Nephrol 19:1197–1203. 10.1681/ASN.2007101058. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  78. [79]Neuhaus TJ, Belzer T, Blau N, Hoppe B, Sidhu H, Leumann E. 2000. Urinary oxalate excretion in urolithiasis and nephrocalcinosis. Arch Dis Child 82:322–326. 10.1136/adc.82.4.322. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  79. [80]Kwak C, Kim HK, Kim EC, Choi MS, Kim HH. 2003. Urinary oxalate levels and the enteric bacterium Oxalobacter formigenes in patients with calcium oxalate urolithiasis. Eur Urol 44:475–481. 10.1016/S0302-2838(03)00318-X. [DOI] [PubMed] [Google Scholar] · DOI
  80. [81]Ticinesi A, Nouvenne A, Meschi T. 2019. Gut microbiome and kidney stone disease: not just an Oxalobacter story. Kidney Int 96:25–27. 10.1016/j.kint.2019.03.020. [DOI] [PubMed] [Google Scholar] · DOI
  81. [82]Abratt VR, Reid SJ. 2010. Oxalate-degrading bacteria of the human gut as probiotics in the management of kidney stone disease. Adv Appl Microbiol 72:63–87. 10.1016/S0065-2164(10)72003-7. [DOI] [PubMed] [Google Scholar] · DOI
  82. [83]Klimesova K, Whittamore JM, Hatch M. 2015. Bifidobacterium animalis subsp. lactis decreases urinary oxalate excretion in a mouse model of primary hyperoxaluria. Urolithiasis 43:107–117. 10.1007/s00240-014-0728-2. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  83. [84]Liu M, Devlin JC, Hu J, Volkova A, Battaglia TW, Ho M, Asplin JR, Byrd A, Loke P, Li H, Ruggles KV, Tsirigos A, Blaser MJ, Nazzal L. 2021. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. Elife 10:e63642. 10.7554/eLife.63642. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  84. [85]Miller AW, Choy D, Penniston KL, Lange D. 2019. Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis. Kidney Int 96:180–188. 10.1016/j.kint.2019.02.012. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  85. [86]Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, Burk R, Davies KP. 2016. Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers. Urolithiasis 44:399–407. 10.1007/s00240-016-0882-9. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  86. [87]Suryavanshi MV, Bhute SS, Gune RP, Shouche YS. 2018. Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease. Sci Rep 8:16598. 10.1038/s41598-018-33773-5. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  87. [88]Suryavanshi MV, Bhute SS, Jadhav SD, Bhatia MS, Gune RP, Shouche YS. 2016. Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures. Sci Rep 6:34712–34715. 10.1038/srep34712. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  88. [89]Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, Wang Q, Yao Z, Mo Z. 2018. 16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones. Urolithiasis 46:503–514. 10.1007/s00240-018-1037-y. [DOI] [PubMed] [Google Scholar] · DOI
  89. [90]Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Dodi R, Dall'Asta M, Del Rio D, Ventura M, Meschi T. 2018. Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut 67:2097–2106. 10.1136/gutjnl-2017-315734. [DOI] [PubMed] [Google Scholar] · DOI
  90. [91]Zampini A, Nguyen AH, Rose E, Monga M, Miller AW. 2019. Defining dysbiosis in patients with urolithiasis. Sci Rep 9:5425. 10.1038/s41598-019-41977-6. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  91. [92]Freter R, Brickner H, Fekete J, Vickerman MM, Carey KE. 1983. Survival and implantation of Escherichia coli in the intestinal tract. Infect Immun 39:686–703. 10.1128/iai.39.2.686-703.1983. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI · Paper page
  92. [93]Mogna L, Pane M, Nicola S, Raiteri E. 2014. Screening of different probiotic strains for their in vitro ability to metabolise oxalates: any prospective use in humans? J Clin Gastroenterol 48 Suppl 1:S91–S95. 10.1097/MCG.0000000000000228. [DOI] [PubMed] [Google Scholar] · DOI
  93. [94]Hatch M, Freel RW. 2013. A human strain of Oxalobacter (HC-1) promotes enteric oxalate secretion in the small intestine of mice and reduces urinary oxalate excretion. Urolithiasis 41:379–384. 10.1007/s00240-013-0601-8. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  94. [95]Arvans D, Jung YC, Antonopoulos D, Koval J, Granja I, Bashir M, Karrar E, Roy-Chowdhury J, Musch M, Asplin J, Chang E, Hassan H. 2017. Oxalobacter formigenes-derived bioactive factors stimulate oxalate transport by intestinal epithelial cells. J Am Soc Nephrol 28:876–887. 10.1681/ASN.2016020132. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  95. [96]Lindner E, Cowley H, Cowley A. 2015. Secretagogues derived from Oxalobacter formigenes. U.S. Patent WO 2015/002588. [Google Scholar]
  96. [97]Duncan SH, Richardson AJ, Kaul P, Holmes RP, Allison MJ, Stewart CS. 2002. Oxalobacter formigenes and its potential role in human health. Appl Environ Microbiol 68:3841–3847. 10.1128/AEM.68.8.3841-3847.2002. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  97. [98]Hoppe B, Beck B, Gatter N, von Unruh G, Tischer A, Hesse A, Laube N, Kaul P, Sidhu H. 2006. Oxalobacter formigenes: a potential tool for the treatment of primary hyperoxaluria type 1. Kidney Int 70:1305–1311. 10.1038/sj.ki.5001707. [DOI] [PubMed] [Google Scholar] · DOI
  98. [99]Hoppe B, Niaudet P, Salomon R, Harambat J, Hulton S-A, Van’t Hoff W, Moochhala SH, Deschênes G, Lindner E, Sjögren A, Cochat P. 2017. 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. 10.1007/s00467-016-3553-8. [DOI] [PubMed] [Google Scholar] · DOI
  99. [100]Milliner D, Hoppe B, Groothoff J. 2018. 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. 10.1007/s00240-017-0998-6. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  100. [101]Panter KE, Ralphs MH, Pfister JA, Gardner DR, Stegelmeier BL, Lee ST, Welch KD, Green BT, Davis TZ, Cook D. 2011. Plants poisonous to livestock in the Western States. Agriculture Bull No415:1–107. U.S. Department of Agriculture, Agricultural Research Service, Poisonous Plant Research Laboratory, Logan, UT. [Google Scholar]
  101. [102]Daniel SL, Hartman PA, Allison MJ. 1987. Intestinal colonization of laboratory rats with Oxalobacter formigenes. Appl Environ Microbiol 53:2767–2770. 10.1128/aem.53.12.2767-2770.1987. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  102. [103]Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar] · DOI
  103. [104]Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035. 10.1073/pnas.0404206101. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  104. [105]Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. 10.1111/j.1558-5646.1985.tb00420.x. [DOI] [PubMed] [Google Scholar] · DOI
  105. [106]Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. 10.1093/molbev/msy096. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  106. [107]Chen IA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, Ritter S, Varghese N, Seshadri R, Roux S, Woyke T, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC. 2021. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res 49:D751–D763. 10.1093/nar/gkaa939. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  107. [108]Ellis ML, Shaw KJ, Jackson SB, Daniel SL, Knight J. 2015. Analysis of commercial kidney stone probiotic supplements. Urology 85:517–521. 10.1016/j.urology.2014.11.013. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  108. [109]Argenzio RA, Liacos JA, Allison MJ. 1988. Intestinal oxalate-degrading bacteria reduce oxalate absorption and toxicity in guinea pigs. J Nutr 118:787–792. 10.1093/jn/118.6.787. [DOI] [PubMed] [Google Scholar] · DOI
  109. [110]Lung HY, Baetz AL, Peck AB. 1994. Molecular cloning, DNA sequence, and gene expression of the oxalyl-coenzyme A decarboxylase gene, oxc, from the bacterium Oxalobacter formigenes. J Bacteriol 176:2468–2472. 10.1128/jb.176.8.2468-2472.1994. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  110. [111]Sidhu H, Ogden SD, Lung H-Y, Luttge BG, Baetz AL, Peck AB. 1997. DNA sequencing and expression of the formyl coenzyme A transferase gene, frc, from Oxalobacter formigenes. J Bacteriol 179:3378–3381. 10.1128/jb.179.10.3378-3381.1997. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  111. [112]Chamberlain CA, Hatch M, Garrett TJ. 2020. Metabolomic alteration in the mouse distal colonic mucosa after oral gavage with Oxalobacter formigenes. Metabolites 10:405. 10.3390/metabo10100405. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI
  112. [113]Smith RL, Strohmaier FE, Oremland RS. 1985. Isolation of anaerobic oxalate-degrading bacteria from freshwater lake sediments. Arch Microbiol 141:8–13. 10.1007/BF00446732. [DOI] [Google Scholar] · DOI
  113. [114]Pareek N. 2019. Evaluation of intra-species diversity of Oxalobacter formigenes strains using pulsed-field gel electrophoresis (PFGE) and multiplex PCR. MS Thesis. Eastern Illinois University, Charleston, IL. [Google Scholar]
  114. [115]Daniel S, Hartman P, Allison M. 1993. Intestinal colonisation of laboratory rats by anaerobic oxalate-degrading bacteria: effects on the urinary and faecal excretion of dietary oxalate. Microb Ecol Health Dis 6:277–283. 10.3109/08910609309141336. [DOI] [Google Scholar] · DOI
  115. [116]Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21. 10.1093/nar/gkw387. [DOI] [PMC free article] [PubMed] [Google Scholar] · DOI

Authors
Daniel, S. L., Moradi, L., Paiste, H., Wood, K. D., Assimos, D. G., Holmes, R. P., Nazzal, L., Hatch, M., & Knight, J.
Affiliations
  • Eastern Illinois University (US)
  • University of Alabama at Birmingham (US)
  • New York University (US)
  • University of Florida (US)
Corresponding author
Daniel, Steven L.
ORCID
Venue
Applied and Environmental Microbiology
Publisher
American Society for Microbiology
Published
2021-08-26
Volume
87
Issue
18
Pages
e0054421-e0054421
ISSN
  • 0099-2240 (ISSN-L)
  • 1098-5336
DOI
10.1128/aem.00544-21
PMC
PMC8388816
OpenAlex
W3177405100
Cited by
88
References
118
Citations by year
2026: 17 · 2025: 23 · 2024: 22 · 2023: 18 · 2022: 8
FWCI
1.26
Type
journal article
Language
en
Open access
Licence
Locations
  • Applied and Environmental Microbiology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (DK-87967, DK-62284)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Kidney Stones and Urolithiasis Treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
Keywords
Oxalobacter formigenes, oxalate degradation, anaerobic bacteria, gut microbiota
MeSH terms
Gastrointestinal Microbiome, Animals, Humans, Inactivation, Metabolic, Oxalates, Oxalobacter formigenes, Genomics, Nephrolithiasis, Metabolomics

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