Oxalobacter formigenes

Oxalobacter formigenes is a Gram negative oxalate-degrading anaerobic bacterium that was first isolated from the gastrointestinal tract of a sheep in 1985.[1] To date, the bacterium has been found to colonizes the large intestines of numerous vertebrates, including humans, and has even been isolated from freshwater sediment.[2] It processes oxalate by decarboxylation into formate (oxalyl-CoA decarboxylase), producing energy for itself in the process.[3]

Oxalobacter formigenes
Scientific classification edit
Domain: Bacteria
Phylum: Pseudomonadota
Class: Betaproteobacteria
Order: Burkholderiales
Family: Oxalobacteraceae
Genus: Oxalobacter
Species:
O. formigenes
Binomial name
Oxalobacter formigenes
Allison et al, 1985[1]
Type strain
Oxalobacter formigenes OxBT

The broad-spectrum quinolone antibiotics kill O. formigenes. If a person's gastrointestinal (GI) tract lacks this bacterium, and therefore lacks the primary source for the oxalyl-CoA decarboxylase enzyme, then the GI tract cannot degrade dietary oxalates which on digestion get absorbed easily and after some vitamin B6-modulated partial metabolic degradation in the body, is excreted in the kidney, where it precipitates with calcium to form calcium oxalate kidney stones.[4][5][6][7] Oxalobacter formigenes can protect against kidney stones by degrading oxalate.[7]

The role and presence of O. formigenes in the human gut is an area of active research.

Genome

The genome of O. formigenes has been sequenced by multiple researchers and is revealed to be 2.41 – 2.47 Mb with a G+C content of 49.6%.[8][9][10]

Taxonomy

Based on fatty acid profile, 16S ribosomal RNA sequencing, and DNA probes specific to the oxc (oxalyl-CoA decarboxylase) gene and frc (formyl-CoA transferase), O. formigenes has been divided into two groups.[1][11][12][13] Group 1 has less diversity and better growth compared to group 2. To date, most research has focused on group 1 strains due to their ease of growth.

Interestingly, analysis with the DNA probes showed that group 2 may be further divided into two subgroups.[12] Whole genome sequencing has revealed that the original O. formigenes taxon can be divided into three additional species: Oxalobacter aliiformigenes, Oxalobacter paeniformigenes, and Oxalobacter paraformigenes.[14]

Growth in culture

O. formigenes was isolated in oxalate containing anerobic media.[1] Currently, O. formigenes is grown in anaerobic Hungate tubes using a CO2-bicarbonate buffered oxalate media.[2] Optimal growth is achieved at a pH between 6 and 7. Oxalate is used at 20 mM for freezer recovery and general maintenance but concentrations can be increased to 100 mM for increased cell density. While oxalate is the main carbon source, small amounts of acetate and yeast extract are supportive of growth.[2] O. formigenes can reach stationary phase in approximately 24 – 48 hours but is sometimes delayed to 72 hours.

Enriched anaerobic complex media (e.g. Brain heart infusion) fail to support the growth of O. formigenes unless supplemented with oxalate. Therefore, these media can be used to assess the purity of O. formigenes cultures.

Antibiotic resistance and susceptibility

Given the fastidious nature of O. formigenes, traditional methods for antibiotic susceptibility testing are not sufficient. Instead, bacteria are cultured in the presence of antibiotics and screened for viability using opaque anaerobic oxalate agar.[2][15][16] This method demonstrated that O. formigenes is resistant to nalidixic acid, ampicillin, amoxicillin, streptomycin, and vancomycin.[15][16] O. formigenes was also found to be susceptible to ciprofloxacin, clarithromycin, clindamycin, doxycycline, gentamicin, levofloxacin, metronidazole, and tetracycline.[15][16]


References
  1. Allison MJ, Dawson KA, Mayberry WR, Foss JG (February 1985). "Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract". Archives of Microbiology. 141 (1): 1–7. doi:10.1007/BF00446731. PMID 3994481. S2CID 10709172.
  2. Daniel SL, Moradi L, Paiste H, Wood KD, Assimos DG, Holmes RP, et al. (August 2021). Pettinari JM (ed.). "Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist". Applied and Environmental Microbiology. 87 (18): e0054421. Bibcode:2021ApEnM..87E.544D. doi:10.1128/AEM.00544-21. PMC 8388816. PMID 34190610.
  3. Unden G (2013). "Energy Transduction in Anaerobic Bacteria". Encyclopedia of Biological Chemistry. pp. 204–209. doi:10.1016/B978-0-12-378630-2.00282-6. ISBN 978-0-12-378631-9.
  4. Troxel SA, Sidhu H, Kaul P, Low RK (2003). "Intestinal Oxalobacter formigenes colonization and urinary oxalate levels in calcium oxalate stone formers". Journal of Endourology. 17 (3): 173–176. doi:10.1089/089277903321618743. PMID 12803990.
  5. Tunuguntla HS (2001). "Can the recurrence of oxalate stones be prevented? Role of Oxalobacter formigenes in stone recurrence". Journal of Urology. 165: S246.
  6. Pearle MS, Goldfarb DS, Assimos DG, Curhan G, Denu-Ciocca CJ, Matlaga BR, et al. (August 2014). "Medical management of kidney stones: AUA guideline". The Journal of Urology. 192 (2): 316–324. doi:10.1016/j.juro.2014.05.006. PMID 24857648.
  7. Siener R, Bangen U, Sidhu H, Hönow R, von Unruh G, Hesse A (June 2013). "The role of Oxalobacter formigenes colonization in calcium oxalate stone disease". Kidney International. 83 (6): 1144–1149. doi:10.1038/ki.2013.104. PMID 23536130.
  8. Sun NY, Gao Y, Yu HJ (October 2019). Stewart FJ (ed.). "Genome Sequence of Oxalobacter formigenes Strain SSYG-15". Microbiology Resource Announcements. 8 (42): e01059–19. doi:10.1128/MRA.01059-19. PMC 6797538. PMID 31624173.
  9. Hatch M, Allison MJ, Yu F, Farmerie W (July 2017). "Genome Sequence of Oxalobacter formigenes Strain OXCC13". Genome Announcements. 5 (28): e00534–17. doi:10.1128/genomeA.00534-17. PMC 5511905. PMID 28705966.
  10. Hatch M, Allison MJ, Yu F, Farmerie W (July 2017). "Genome Sequence of Oxalobacter formigenes Strain HC-1". Genome Announcements. 5 (27): e00533–17. doi:10.1128/genomeA.00533-17. PMC 5502849. PMID 28684568.
  11. Jensen, N.S.; Allison, M.J. (1994). "Studies on the diversity among anaerobic oxalate-degrading bacteria now in the species Oxalobacter formigenes, abstr. I-12". Abstracts of the 94th General Meeting of the American Society for Microbiology 1994. Washington, D.C., USA: American Society for Microbiology. p. 255.
  12. Sidhu, H; Allison, M; Peck, A B (1997). "Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers". Journal of Clinical Microbiology. 35 (2): 350–353. doi:10.1128/jcm.35.2.350-353.1997. ISSN 0095-1137. PMC 229578. PMID 9003594.
  13. Garrity, George M.; Bell, Julia A.; Lilburn, Timothy (2005), Brenner, Don J.; Krieg, Noel R.; Staley, James T. (eds.), "Class II. Betaproteobacteria class. nov.", Bergey’s Manual® of Systematic Bacteriology, Boston, MA: Springer US, pp. 575–922, doi:10.1007/978-0-387-29298-4_2, ISBN 978-0-387-24145-6, retrieved 2022-11-10
  14. Chmiel, John A.; Carr, Charles; Stuivenberg, Gerrit A.; Venema, Robertson; Chanyi, Ryan M.; Al, Kait F.; Giguere, Daniel; Say, Henry; Akouris, Polycronis P.; Domínguez Romero, Sergio Ari; Kwong, Aaron; Tai, Vera; Koval, Susan F.; Razvi, Hassan; Bjazevic, Jennifer (2022-12-21). "New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention". Frontiers in Microbiology. 13: 1011102. doi:10.3389/fmicb.2022.1011102. ISSN 1664-302X. PMC 9812493. PMID 36620050.
  15. Duncan SH, Richardson AJ, Kaul P, Holmes RP, Allison MJ, Stewart CS (August 2002). "Oxalobacter formigenes and its potential role in human health". Applied and Environmental Microbiology. 68 (8): 3841–3847. Bibcode:2002ApEnM..68.3841D. doi:10.1128/AEM.68.8.3841-3847.2002. PMC 124017. PMID 12147479.
  16. Lange JN, Wood KD, Wong H, Otto R, Mufarrij PW, Knight J, et al. (June 2012). "Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics". Urology. 79 (6): 1286–1289. doi:10.1016/j.urology.2011.11.017. PMC 3569510. PMID 22656407.
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