Oxalobacter paraformigenes

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]

Oxalobacter paraformigenes
Scientific classification
Domain:	Bacteria
Kingdom:	Pseudomonadati
Phylum:	Pseudomonadota
Class:	Betaproteobacteria
Order:	Burkholderiales
Family:	Oxalobacteraceae
Genus:	Oxalobacter
Species:	O. paraformigenes
Binomial name
Oxalobacter paraformigenes Chmiel et al, 2022
Type strain
Oxalobacter paraformigenes HOxBLST

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][5] However, whole genome sequencing revealed that O. paraformigenes HOxBLS is a different species from O. formigenes and it was subsequently renamed.^[6] The new species name paraformigenes uses the parent species formigenes and adds the Greek prefix para meaning "beside",^[7] 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).^[6]

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%.^[8][9] O. paraformigenes has a slightly higher G+C content than O. formigenes and slightly more gene sequences.^[1][6][10]

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