Oxalobacter paraformigenes

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Oxalobacter paraformigenes
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
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

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]

Contents

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]

Related Research Articles

<span class="mw-page-title-main">Oxalic acid</span> Simplest dicarboxylic acid

Oxalic acid is an organic acid with the systematic name ethanedioic acid and formula HO2C−CO2H, also written as (CO2H)2. It is the simplest dicarboxylic acid. It is a white crystalline solid that forms a colorless solution in water. Its name comes from the fact that early investigators isolated oxalic acid from flowering plants of the genus Oxalis, commonly known as wood-sorrels. It occurs naturally in many foods. Excessive ingestion of oxalic acid or prolonged skin contact can be dangerous.

<span class="mw-page-title-main">Acidobacteriota</span> Phylum of bacteria

Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.

<span class="mw-page-title-main">Oxalate</span> Any derivative of oxalic acid; chemical compound containing oxalate moiety

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 oxalate (C2O4(CH3)2). It is a conjugate base of oxalic acid. At neutral pH in aqueous solution, oxalic acid converts completely to oxalate.

<i>Proteus mirabilis</i> Species of bacterium

Proteus mirabilis is a Gram-negative, facultatively anaerobic, rod-shaped bacterium. It shows swarming motility and urease activity. P. mirabilis causes 90% of all Proteus infections in humans. It is widely distributed in soil and water. Proteus mirabilis can migrate across the surface of solid media or devices using a type of cooperative group motility called swarming. Proteus mirabilis is most frequently associated with infections of the urinary tract, especially in complicated or catheter-associated urinary tract infections.

Ferroglobus is a genus of the Archaeoglobaceae.

<i>Lacticaseibacillus casei</i> Species of bacterium

Lacticaseibacillus casei is an organism that belongs to the largest genus in the family Lactobacillaceae, a lactic acid bacteria (LAB), that was previously classified as Lactobacillus casei. This bacteria has been identified as facultatively anaerobic or microaerophilic, acid-tolerant, non-spore-forming bacteria.

Organohalide respiration (OHR) (previously named halorespiration or dehalorespiration) is the use of halogenated compounds as terminal electron acceptors in anaerobic respiration. Organohalide respiration can play a part in microbial biodegradation. The most common substrates are chlorinated aliphatics (PCE, TCE, chloroform) and chlorinated phenols. Organohalide-respiring bacteria are highly diverse. This trait is found in some Campylobacterota, Thermodesulfobacteriota, Chloroflexota (green nonsulfur bacteria), low G+C gram positive Clostridia, and ultramicrobacteria.

Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.

Dehalococcoides is a genus of bacteria within class Dehalococcoidia that obtain energy via the oxidation of hydrogen and subsequent reductive dehalogenation of halogenated organic compounds in a mode of anaerobic respiration called organohalide respiration. They are well known for their great potential to remediate halogenated ethenes and aromatics. They are the only bacteria known to transform highly chlorinated dioxins, PCBs. In addition, they are the only known bacteria to transform tetrachloroethene to ethene.

Oxalobacter formigenes is a Gram negative oxalate-degrading anaerobic bacterium that was first isolated from the gastrointestinal tract of a sheep in 1985. To date, the bacterium has been found to colonize the large intestines of numerous vertebrates, including humans, and has even been isolated from freshwater sediment. It processes oxalate by decarboxylation into formate, producing energy for itself in the process.

"Aromatoleum" is a genus of bacteria capable of microbial biodegradation of organic pollutants. It has one single described species member, A. aromaticum, for which the only strain is strain EbN1.

Oxalobacter is a genus of bacteria in the Oxalobacteraceae family. The species are chemoorganotrophs and strictly anaerobic. They are found in rumens of animals such as cattle and in feces of other animals and humans. Some are marine and some have been isolated from fresh water. These bacteria are characterized by their ability to metabolize oxalate.

<i>Cytophaga</i> Genus of bacteria

Cytophaga is a genus of Gram-negative, gliding, rod-shaped bacteria. This bacterium is commonly found in soil, rapidly digests crystalline cellulose C. hutchinsonii is able to use its gliding motility to move quickly over surfaces. Although the mechanism for this is not known, there is a belief that the flagellum is not used

Oxalobacter vibrioformis is an oxalate-degrading anaerobic bacterium that was isolated from anoxic freshwater sediments. O. vibrioformis is a Gram-negative, non-spore-forming, motile, vibrioid rod which belongs to the genus Oxalobacter. O. vibrioformis uses oxalate and oxamate as its sole source of energy and acetate as its main source of carbon.

Ruminiclostridium cellobioparum is a species of anaerobic cellulose-degrading Gram-positive bacterium found in the bovine rumen belonging to the family Oscillospiraceae.

Desulfitobacterium dehalogenans is a species of bacteria. They are facultative organohalide respiring bacteria capable of reductively dechlorinating chlorophenolic compounds and tetrachloroethene. They are anaerobic, motile, Gram-positive and rod-shaped bacteria capable of utilizing a wide range of electron donors and acceptors. The type strain JW/IU-DCT, DSM 9161, NCBi taxonomy ID 756499.

Oxalotrophic bacteria are bacteria capable of using oxalate as their sole source of carbon and energy. Oxalate is the anion of a salt of oxalic acid; oxalotrophs often consume calcium oxalate. Oxalotrophic bacteria are often facultative methylotrophs.

Cytophagales is an order of non-spore forming, rod-shaped, Gram-negative bacteria that move through a gliding or flexing motion. These chemoorganotrophs are important remineralizers of organic materials into micronutrients. They are widely dispersed in the environment, found in ecosystems including soil, freshwater, seawater and sea ice. Cytophagales is included in the Bacteroidota phylum.

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

<i>Phocaeicola vulgatus</i> Species of bacteria

Phocaeicola vulgatus,, is a mutualistic anaerobic Gram negative rod bacteria commonly found in the human gut microbiome and isolated from feces. P. vulgatus has medical relevance and has been notable in scientific research due to its production of fatty acids, potential use as a probiotic, and associations with protecting against and worsening some inflammatory diseases. Due to the difficulties in culturing anaerobic bacteria, P. vulgatus is still highly uncharacterised so efforts are being made to make use of multi-omic approaches to investigate the human gut microbiome more thoroughly in hopes to fully understand the role of this species in the development of and protection against diseases, as well as its potential uses in medicine and research. Generally, P. vulgatus is considered as a beneficial bacteria that contributes to digestion and a balanced microbiome, but it has been known to cause opportunistic infections and induce or worsen inflammatory responses. Due to its abundance in the microbiome, some researchers are investigating these species in hopes that it will be a suitable model organism for gut microbiome research, like Bacteroides thetaiotaomicron.

References

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