Oxalobacter paraformigenes

Oxalobacter paraformigenes is a Gram negative, non-spore-forming, oxalate-degrading anaerobic bacterium that was first isolated from human fecal samples.[1] O. paraformigenes may have a role in calcium oxalate kidney stone disease because of its unique ability to utilize oxalate as its primary carbon source.[1]

Oxalobacter paraformigenes
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Betaproteobacteria
Order: Burkholderiales
Family: Oxalobacteraceae
Genus: Oxalobacter
Species:
O. paraformigenes
Binomial name
Oxalobacter paraformigenes
Chmiel et al, 2022
Type strain
Oxalobacter paraformigenes HOxBLST

Taxonomy

Oxalobacter paraformigenes was originally thought to be a subgroup of Oxalobacter formigenes.[1] 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. paraformigenes strain HOxBLS was considered a group II strain.[2][3][4][5] However, whole genome sequencing revealed that O. paraformigenes HOxBLS is a different species from O. formigenes and it was subsequently renamed.[6] The new species name paraformigenes uses the parent species formigenes and adds the Greek prefix para meaning "beside",[7] owing to that for the longest time O. paraformigenes was the only group II strain with a full genome sequence and it was used to make genetic comparisons between group I strains (now known as O. formigenes).[6]

Genome

The genome of O. paraformigenes was sequenced as part of the Human Microbiome Project and is approximately 2.5 Mb with a G+C content of approximately 52.7%.[8][9] O. paraformigenes has a slightly higher G+C content than O. formigenes and slightly more gene sequences.[1][6][10]

Growth in culture

O. paraformigenes grows in CO2-bicarbonate buffered oxalate media and is typically cultivated in anaerobic Hungate tubes or an anaerobic chamber.[1] Oxalate is supplemented at 20 – 100 mM (depending on desired cell density) and bacteria are grown at 37 °C for 24 – 48 hours.[1][6] Anaerobic roll tubes, which are opaque agar filled Hungate tubes are used for bacterial isolation.[1]

References
  1. Daniel, Steven L.; Moradi, Luke; Paiste, Henry; Wood, Kyle D.; Assimos, Dean G.; Holmes, Ross P.; Nazzal, Lama; Hatch, Marguerite; Knight, John (2021-08-26). Julia Pettinari, M. (ed.). "Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist". Applied and Environmental Microbiology. 87 (18). doi:10.1128/AEM.00544-21. ISSN 0099-2240. PMC 8388816. PMID 34190610.
  2. 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.
  3. 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.
  4. 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
  5. Sidhu, H; Enatska, L; Ogden, S; Williams, W; Allison, M; Peck, A (June 1997). "Evaluating children in the Ukraine for colonization with the intestinal bacterium Oxalobacter formigenes, using a polymerase chain reaction-based detection system*". Molecular Diagnosis. 2 (2): 89–97. doi:10.1016/S1084-8592(97)80015-X.
  6. 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.
  7. Pallen, Mark J.; Telatin, Andrea; Oren, Aharon (April 2021). "The Next Million Names for Archaea and Bacteria". Trends in Microbiology. 29 (4): 289–298. doi:10.1016/j.tim.2020.10.009.
  8. 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. doi:10.3389/fmicb.2022.1011102. ISSN 1664-302X. PMC 9812493. PMID 36620050.
  9. "MIGS Cultured Bacterial/Archaeal sample from Oxalo... - BioSample - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2023-10-23.
  10. Knight, John; Deora, Rajendar; Assimos, Dean G.; Holmes, Ross P. (June 2013). "The genetic composition of Oxalobacter formigenes and its relationship to colonization and calcium oxalate stone disease". Urolithiasis. 41 (3): 187–196. doi:10.1007/s00240-013-0566-7. ISSN 2194-7228. PMC 3713771. PMID 23632911.
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