Oxalobacter paeniformigenes explained

Oxalobacter paeniformigenes is a Gram negative, non-spore-forming, oxalate-degrading anaerobic bacterium that was first isolated from human fecal samples.^[1] Similar to other species in the Oxalobacter genus, O. paeniformigenes uses oxalate as its primary carbon source.^[1] O. paeniformigenes is negative for indole production and negative for sulfate and nitrate reduction. Cells appear rod shaped, though occasionally present as curved, and do not possess flagella.

The Type strain, OxGP1, was isolated from Guinea pig cecal contents.^[2]

Taxonomy

Oxalobacter paeniformigenes was originally thought to be a subgroup of Oxalobacter formigenes.^[1] Based on fatty acid profile and oxc (oxalyl-CoA decarboxylase) gene analysis, O. paeniformigenes strain OxGP1 was considered a group II strain.^{[3] [4]} However, 16S ribosomal RNA sequencing placed strain OxGP1 into group I.

Whole genome sequencing confirmed that O. paeniformigenes strain OxGP1 is a different species from O. formigenes and it was subsequently renamed.^[5] The new species name paeniformigenes uses the parent species formigenes and adds the Latin prefix paeni meaning "almost",^[6] owing to the observation that species is related to but distinct from the parent species, O. formigenes.

Genome

The genome of O. paeniformigenes is approximately 1.9 Mb with a G+C content of approximately 53.8%. O. paeniformigenes has a smaller genome with slightly higher G+C content compared to other Oxalobacter species.

Growth in culture

O. paeniformigenes 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

• NCBI taxonomy browser
• ATCC TSD-347
• DSM 115066
  

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. Argenzio . Robert A. . Liacos . James A. . Allison . Milton J. . June 1988 . Intestinal Oxalate-Degrading Bacteria Reduce Oxalate Absorption and Toxicity in Guinea Pigs . The Journal of Nutrition . en . 118 . 6 . 787–792 . 10.1093/jn/118.6.787.
3. 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.
4. 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.
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 .