Oxalobacter paraformigenes explained

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]

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] However, whole genome sequencing revealed that O. paraformigenes HOxBLS is a different species from O. formigenes and it was subsequently renamed.[5] The new species name paraformigenes uses the parent species formigenes and adds the Greek prefix para meaning "beside",[6] 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).[5]

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%.[7] [8] O. paraformigenes has a slightly higher G+C content than O. formigenes and slightly more gene sequences.[1] [5] [9]

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] [5] Anaerobic roll tubes, which are opaque agar filled Hungate tubes are used for bacterial isolation.[1]

External links

Notes and 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. . Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist . Applied and Environmental Microbiology . en . 87 . 18 . e0054421 . 10.1128/AEM.00544-21 . 0099-2240 . 8388816 . 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 . 10.1007/BF00446731 . 3994481 . 10709172.
  3. Book: Jensen . N.S. . Abstracts of the 94th General Meeting of the American Society for Microbiology 1994 . Allison . M.J. . American Society for Microbiology . 1994 . Washington, D.C., USA . 255 . Studies on the diversity among anaerobic oxalate-degrading bacteria now in the species Oxalobacter formigenes, abstr. I-12.
  4. 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 . en . 2 . 2 . 89–97 . 10.1016/S1084-8592(97)80015-X.
  5. 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 . 10.3389/fmicb.2022.1011102 . 36620050 . 9812493 . 1664-302X. free .
  6. Pallen . Mark J. . Telatin . Andrea . Oren . Aharon . April 2021 . The Next Million Names for Archaea and Bacteria . Trends in Microbiology . en . 29 . 4 . 289–298 . 10.1016/j.tim.2020.10.009. free .
  7. 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 . 10.3389/fmicb.2022.1011102 . 1664-302X . 9812493 . 36620050 . free .
  8. Web site: MIGS Cultured Bacterial/Archaeal sample from Oxalo... - BioSample - NCBI . 2023-10-23 . www.ncbi.nlm.nih.gov.
  9. 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 . en . 41 . 3 . 187–196 . 10.1007/s00240-013-0566-7 . 2194-7228 . 3713771 . 23632911.

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