''Oxalobacter formigenes'' is a

Gram negative The gram (originally gramme; SI unit symbol g) is a unit of mass in the International System of Units (SI) equal to one one thousandth of a kilogram. Originally defined as of 1795 as "the absolute weight of a volume of pure water equal to th ...

oxalate Oxalate (IUPAC: ethanedioate) is an anion with the formula C2O42−. This dianion is colorless. It occurs naturally, including in some foods. It forms a variety of salts, for example sodium oxalate (Na2C2O4), and several esters such as dimethyl o ...

-degrading

anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...

bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

that was first isolated from the gastrointestinal tract of a sheep in 1985. To date, the bacterium has been found to colonizes the

large intestine The large intestine, also known as the large bowel, is the last part of the gastrointestinal tract and of the digestive system in tetrapods. Water is absorbed here and the remaining waste material is stored in the rectum as feces before being r ...

s of numerous

vertebrate Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...

s, including humans, and has even been isolated from freshwater sediment. It processes oxalate by

decarboxylation Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is t ...

into

formate Formate (IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless.Werner Reutemann and Heinz Kieczka "Formic Acid" in ''Ull ...

( oxalyl-CoA decarboxylase), producing energy for itself in the process. The broad-spectrum

quinolone antibiotic A quinolone antibiotic is a member of a large group of broad-spectrum bacteriocidals that share a bicyclic core structure related to the substance 4-quinolone. They are used in human and veterinary medicine to treat bacterial infections, as we ...

s kill ''O. formigenes''. If a person's gastrointestinal (GI) tract lacks this bacterium, and therefore lacks the primary source for the oxalyl-CoA decarboxylase enzyme, then the GI tract cannot degrade dietary oxalates which on digestion get absorbed easily and after some vitamin B₆-modulated partial metabolic degradation in the body, is excreted in the kidney, where it precipitates with calcium to form calcium oxalate

kidney stone Kidney stone disease, also known as nephrolithiasis or urolithiasis, is a crystallopathy where a solid piece of material (kidney stone) develops in the urinary tract. Kidney stones typically form in the kidney and leave the body in the urine s ...

s. ''Oxalobacter formigenes'' can protect against kidney stones by degrading oxalate. The role and presence of ''O. formigenes'' in the human gut is an area of active research.

Genome

The genome of ''O. formigenes'' has been sequenced by multiple researchers and is revealed to be 2.41 – 2.47 Mb with a G+C content of 49.6%.

Taxonomy

Based on

fatty acid In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms, fr ...

profile,

16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA ...

sequencing, and DNA probes specific to the ''oxc'' ( oxalyl-CoA decarboxylase) gene and ''frc'' (formyl-CoA transferase), ''O. formigenes'' has been divided into two groups. Group 1 has less diversity and better growth compared to group 2. To date, most research has focused on group 1 strains due to their ease of growth. Interestingly, analysis with the DNA probes showed that group 2 may be further divided into two subgroups. Whole genome sequencing has revealed that the original ''O. formigenes'' taxon can be divided into three additional species: ''Oxalobacter aliiformigenes'', '' Oxalobacter paeniformigenes'', and '' Oxalobacter paraformigenes''.

Growth in culture

''O. formigenes'' was isolated in oxalate containing anerobic media. Currently, ''O. formigenes'' is grown in anaerobic Hungate tubes using a CO₂-bicarbonate buffered oxalate media. Optimal growth is achieved at a pH between 6 and 7. Oxalate is used at 20 mM for freezer recovery and general maintenance but concentrations can be increased to 100 mM for increased cell density. While oxalate is the main carbon source, small amounts of

acetate An acetate is a salt (chemistry), salt formed by the combination of acetic acid with a base (e.g. Alkali metal, alkaline, Alkaline earth metal, earthy, Transition metal, metallic, nonmetallic or radical Radical (chemistry), base). "Acetate" als ...

and

yeast extract Yeast extracts consist of the cell contents of yeast without the cell walls; they are used as food additives or flavorings, or as nutrients for bacterial culture media. They are often used to create savory flavors and umami taste sensations, a ...

are supportive of growth. ''O. formigenes'' can reach stationary phase in approximately 24 – 48 hours but is sometimes delayed to 72 hours. Enriched anaerobic complex media (e.g.

Brain heart infusion Brain heart infusion (BHI) is a growth medium for growing microorganisms. It is a nutrient-rich medium, and can therefore be used to culture a variety of fastidious organisms. In particular, it has been used to culture streptococci, pneumococci an ...

) fail to support the growth of ''O. formigenes'' unless supplemented with oxalate. Therefore, these media can be used to assess the purity of ''O. formigenes'' cultures.

Antibiotic resistance and susceptibility

Given the fastidious nature of ''O. formigenes'', traditional methods for antibiotic susceptibility testing are not sufficient. Instead, bacteria are cultured in the presence of antibiotics and screened for viability using opaque anaerobic oxalate agar. This method demonstrated that ''O. formigenes'' is resistant to nalidixic acid, ampicillin, amoxicillin, streptomycin, and vancomycin. ''O. formigenes'' was also found to be susceptible to ciprofloxacin, clarithromycin, clindamycin, doxycycline, gentamicin, levofloxacin, metronidazole, and tetracycline.

References

Burkholderiales {{Betaproteobacteria-stub