Biology:Oxalobacter aliiformigenes
| 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 | |
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]
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]
References
- ↑ 1.0 1.1 "Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract". Archives of Microbiology 141 (1): 1–7. February 1985. doi:10.1007/BF00446731. PMID 3994481.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Chmiel, John A.; Carr, Charles; Stuivenberg, Gerrit A.; Venema, Robertson; Chanyi, Ryan M.; Al, Kait F.; Giguere, Daniel; Say, Henry et al. (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. PMID 36620050.
- ↑ 3.0 3.1 3.2 3.3 3.4 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" (in en). Applied and Environmental Microbiology 68 (8): 3841–3847. doi:10.1128/AEM.68.8.3841-3847.2002. ISSN 0099-2240. 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" (in en). The Journal of Nutrition 116 (3): 455–460. doi:10.1093/jn/116.3.455. https://linkinghub.elsevier.com/retrieve/pii/S0022316623077581.
- ↑ 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. pp. 255.
- ↑ Sidhu, H; Allison, M; Peck, A B (1997). "Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers" (in en). Journal of Clinical Microbiology 35 (2): 350–353. doi:10.1128/jcm.35.2.350-353.1997. ISSN 0095-1137. 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." (in en), 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, http://link.springer.com/10.1007/0-387-29298-5_2, retrieved 2022-11-10
- ↑ "Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics". Urology 79 (6): 1286–1289. June 2012. doi:10.1016/j.urology.2011.11.017. PMID 22656407.
- ↑ 9.0 9.1 9.2 Daniel, Steven L.; Moradi, Luke; Paiste, Henry; Wood, Kyle D.; Assimos, Dean G.; Holmes, Ross P.; Nazzal, Lama; Hatch, Marguerite et al. (2021-08-26). Julia Pettinari, M.. ed. "Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist" (in en). Applied and Environmental Microbiology 87 (18). doi:10.1128/AEM.00544-21. ISSN 0099-2240. PMID 34190610. PMC 8388816. https://journals.asm.org/doi/10.1128/AEM.00544-21.
External links
- NCBI taxonomy browser
- https://www.atcc.org/products/tsd-348
- https://www.dsmz.de/collection/catalogue/details/culture/DSM-115068
Wikidata ☰ Q116263385 entry
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