Oxalobacter aliiformigenes

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Oxalobacter aliiformigenes
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Phylum: Pseudomonadota
Class: Betaproteobacteria
Order: Burkholderiales
Family: Oxalobacteraceae
Genus: Oxalobacter
Species:
O. aliiformigenes
Binomial name
Oxalobacter aliiformigenes
Chmiel et al, 2022
Type strain
Oxalobacter aliiformigenes Va3T

Oxalobacter aliiformigenes is a Gram negative, non-spore-forming, oxalate-degrading anaerobic bacterium that was first isolated from human fecal samples. [1] O. aliiformigenes consumes oxalate as its main carbon source but is negative for indole production and negative for sulfate and nitrate reduction. [2] Cells appear rod shaped, though occasionally present as curved, and do not possess flagella. [2]

Contents

O. aliiformigenes is found in the gastrointestinal tract of humans, and is typically isolated from human feces. O. aliiformigenes is believed to have roles in mitigating calcium oxalate kidney stone disease and primary hyperoxaluria because of its unique ability to utilize oxalate as its primary carbon source and prevent absorption of oxalate. [3] [4]

Taxonomy

Oxalobacter aliiformigenes was originally thought to be a subgroup of Oxalobacter formigenes 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). [1] [5] [6] [7] However, full genomes were sequenced and based on average nucleotide identity calculation, digital DNA-DNA hybridization, and phylogenetic tree analyses, O. aliiformigenes was determined to be a distinct species. [2]

Antibiotic resistance and susceptibility

Oxalobacter aliiformigenes demonstrates in vitro resistance to amoxicillin, ampicillin, ceftriaxone, cephalexin, streptomycin, and vancomycin; and in vitro sensitivity to clarithromycin, clindamycin, ciprofloxacin, doxycycline, gentamicin, and tetracycline. [3] [8]

Genome

The genome of O. aliiformigenes has been sequenced and is 2.2 – 2.4 Mb with a G+C content of 50.9 - 51.5%. [2] Beta-lactamase genes present in the genome may provide resistance to beta-lactam antibiotics. [2]

Growth in Culture

O. aliiformigenes grows in CO2-bicarbonate buffered oxalate media and is typically cultivated in anaerobic Hungate tubes or an anaerobic chamber. [9] Oxalate is supplemented at 20 – 100 mM (depending on desired cell density) and bacteria are grown at 37 °C for 24 – 72 hours. [2] [9] Acetate is required for cultivation but does not support growth alone. Bacteria can grow adequately in pH ranges of 7.0 - 2.0. [3] Higher concentrations of bile salts impair growth but lower concentrations are tolerated. [3] The species can tolerate some levels of oxygen but cell numbers are diminished. [3]

Bacteria are isolated using anaerobic roll tubes, which are Hungate tubes filled with opaque oxalate agar media that display zones of clearance upon successful Oxalobacter cultivation. [9]

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References

  1. 1 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.
  2. 1 2 3 4 5 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.
  3. 1 2 3 4 5 Duncan, Sylvia H.; Richardson, Anthony J.; Kaul, Poonam; Holmes, Ross P.; Allison, Milton J.; Stewart, Colin S. (2002). "Oxalobacter formigenes and its potential role in human health". Applied and Environmental Microbiology. 68 (8): 3841–3847. doi:10.1128/AEM.68.8.3841-3847.2002. ISSN   0099-2240. PMC   124017 . PMID   12147479.
  4. ↑ Allison, Milton J.; Cook, Herbert M.; Milne, David B.; Gallagher, Sandra; Clayman, Ralph V. (March 1986). "Oxalate Degradation by Gastrointestinal Bacteria from Humans". The Journal of Nutrition. 116 (3): 455–460. doi: 10.1093/jn/116.3.455 .
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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
  8. ↑ 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.
  9. 1 2 3 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.
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