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]
| Oxalobacter aliiformigenes | |
|---|---|
Scientific classification 
| |
| 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 | |
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
editOxalobacter 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
editOxalobacter 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
editThe 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
editO. 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]
References
edit- ^ a b 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.
- ^ a b c d e f 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.
- ^ a b c d e 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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
- ^ 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.
- ^ a b c 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.