Oxalobacter formigenes

Genome

The genome of O. formigenes has been sequenced by at least three different researchers. It has a G+C content of 49.6%.

Taxonomy

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. 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.

Metabolism

O. formigenes uses oxalate as its primary carbon source. Oxalate is absorbed through an oxalate:formate antiporter (OxlT) in a 1:1 proportion. Imported oxalate is then converted to oxalyl-CoA via formyl-CoA transferase (frc). Oxalyl-CoA is decarboxylated using and H+ via oxalyl-CoA decarboxylase (oxc), releasing CO2, and generating formyl-CoA, which is used for the frc reaction. In total, approximately 1 mol of formate and CO2 are produced per mol of oxalate consumed. 3H+ are imported via an ATPase to provide H+ for the decarboxylation reaction.

Cell biomass generation

Biomass in O. formigenes is primarily generated by oxalate consumption through the metabolism of oxalyl-CoA in the glycerate pathway. Acetate and carbonate are also used for cell biomass, but to a lesser extent than oxalate.

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 and yeast extract 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) 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.

Prevalence in the mammalian gut

O. formigenes is found in the mammalian gastrointestinal tract and often isolated from feces. In addition to culture-based methods, O. formigenes is presence is detected using molecular methods such as qPCR and next generation sequencing.

Humans

Humans are not typically born with O. formigenes and only become colonized when they begin crawling around in their environment. In adulthood, the frequency of O. formigenes in the gut microbiota varies across different populations. In North India, O. formigenes is prevalent in approximately 65% of the population. In South Korea and Japan, O. formigenes is present in about 75% of individuals. In the United States of America, O. formigenes is only detected in about 30% of the human population. Populations who do not practice modern medicine or life in a Western lifestyle typically have an increased prevalence of O. formigenes, which could imply that these practices affect O. formigenes colonization.

Ruminants

The idea that ruminants are colonized by oxalate-degrading bacteria came from the observation that sheep grazing on oxalate-rich plants (e.g. Halogeton glomeratus) consumed large quantities of this plant and died of renal intoxication from oxalate. However, by slowly acclimatizing sheep to high-oxalate intake, they would survive the consumption of large quantities of oxalate-rich plants. This led to the proposal that resident oxalate-degrading bacteria were enriched by the gradual introduction to an oxalate-rich diet, which protected the sheep from oxalate-induced renal damage. In 1980, the first oxalate-degrading bacteria were isolated from the rumen of sheep, and it was later named Oxalobacter formigenes.

Clinical significance

O. formigenes has been investigated for its role in mitigating calcium oxalate kidney stone disease and primary hyperoxaluria because it metabolizes oxalate as its primary carbon source.

Oxalate degradation in kidney stone disease

In vitro experiments find that O. formigenes is a specialist oxalate-consuming bacterium that can degrade oxalate more efficiently than other generalist oxalate consuming bacteria. Initial research pointed to the loss of oxalate-degrading bacteria, such as O. formigenes, following antibiotic usage as primary contributor to calcium oxalate kidney stone disease. Colonization with O. formigenes has been observed to result in a decrease in urinary oxalate and reduced frequency of kidney stones.

Recent work using next-generation sequencing has found that O. formigenes colonizes both calcium oxalate kidney stone formers and non-stone-forming controls. This observation has led to the notion that O. formigenes alone may not be responsible for regulating oxalate degradation in the gut microbiota, but instead it may be part of a network of co-occurring bacterial taxa that modulate oxalate degradation together.

Secretagogues to promote intestinal oxalate dumping in kidney stone disease

It has been proposed that O. formigenes produces secretagogues that can stimulate oxalate transport in epithelial cells. While epithelial oxalate secretion has been shown in human cell lines and rodent models, it has not been confirmed in humans. Candidate bioactive molecules have been identified and tested in animal models.

''O. formigenes'' as a therapeutic for primary hyperoxaluria

In a small study, oral supplementation with O. formigenes HC-1 along with a loading dose of oxalate resulted in reduced oxalate excretion during the 6 h immediately following ingestion. Multiple clinical trials in populations with primary hyperoxaluria have demonstrated that O. formigenes supplementation is safe and well tolerated but data are mixed on the capability of O. formigenes to establish in hosts and reduce urinary and plasma concentrations of oxalate.

Typing

Pathogenicity

References

References

1. (February 1985). "Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract". Archives of Microbiology.
2. (August 2021). "Forty Years of Oxalobacter formigenes, a Gutsy Oxalate-Degrading Specialist". Applied and Environmental Microbiology.
3. (2013). "Encyclopedia of Biological Chemistry".
4. (2001). "Can the recurrence of oxalate stones be prevented? Role of Oxalobacter formigenes in stone recurrence.". Journal of Urology.
5. (August 2014). "Medical management of kidney stones: AUA guideline". The Journal of Urology.
6. (June 2013). "The role of Oxalobacter formigenes colonization in calcium oxalate stone disease". Kidney International.
7. (October 2019). "Genome Sequence of Oxalobacter formigenes Strain SSYG-15". Microbiology Resource Announcements.
8. (July 2017). "Genome Sequence of ''Oxalobacter formigenes'' Strain OXCC13". Genome Announcements.
9. (July 2017). "Genome Sequence of ''Oxalobacter formigenes'' Strain HC-1". Genome Announcements.
10. (1994). "Studies on the diversity among anaerobic oxalate-degrading bacteria now in the species ''Oxalobacter formigenes'', abstr. I-12". American Society for Microbiology.
11. (February 1997). "Identification and classification of Oxalobacter formigenes strains by using oligonucleotide probes and primers". Journal of Clinical Microbiology.
12. (2005). "Bergey's Manual® of Systematic Bacteriology". Springer US.
13. (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.
14. (1989). "Oxalate:formate exchange". Journal of Biological Chemistry.
15. (1996). "Generation of a proton motive force by the anaerobic oxalate-degrading bacterium Oxalobacter formigenes". Applied and Environmental Microbiology.
16. (1996). "Assimilation of oxalate, acetate, and CO 2 by Oxalobacter formigenes". Canadian Journal of Microbiology.
17. (1996). "Anabolic Incorporation of Oxalate by Oxalobacter formigenes". Applied and Environmental Microbiology.
18. (August 2002). "Oxalobacter formigenes and its potential role in human health". Applied and Environmental Microbiology.
19. (June 2012). "Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics". Urology.
20. (June 1997). "Evaluating Children in the Ukraine for Colonization With the Intestinal Bacterium Oxalobacter formigenes, Using a Polymerase Chain Reaction-based Detection System". Molecular Diagnosis.
21. (March 2002). "Role of Oxalobacter formigenes in calcium oxalate stone disease: a study from North India". European Urology.
22. (May 2003). "Molecular epidemiology of fecal Oxalobacter formigenes in healthy adults living in Seoul, Korea". Journal of Endourology.
23. (July 2003). "[Detection of Oxalobacter formigenes in human feces and study of related genes in a new oxalate-degrading bacterium]". Hinyokika Kiyo. Acta Urologica Japonica.
24. (February 2016). "The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults". The Journal of Urology.
25. (April 2011). "Factors related to colonization with Oxalobacter formigenes in U.S. adults". Journal of Endourology.
26. (January 2019). "Comparative prevalence of Oxalobacter formigenes in three human populations". Scientific Reports.
27. (April 2015). "The microbiome of uncontacted Amerindians". Science Advances.
28. (November 1974). "Management practices to minimize death losses of sheep grazing Halogeton-infested range". Journal of Range Management.
29. (November 1977). "Changes in ruminal oxalate degradation rates associated with adaptation to oxalate ingestion". Journal of Animal Science.
30. (August 1989). "Enumeration of anaerobic oxalate-degrading bacteria in the ruminal contents of sheep". FEMS Microbiology Letters.
31. (October 1980). "Isolation and some characteristics of anaerobic oxalate-degrading bacteria from the rumen". Applied and Environmental Microbiology.
32. (September 2004). "Characterization and heterologous expression of the oxalyl coenzyme A decarboxylase gene from Bifidobacterium lactis". Applied and Environmental Microbiology.
33. (September 1998). "Absence of Oxalobacter formigenes in cystic fibrosis patients: a risk factor for hyperoxaluria". Lancet.
34. (January 2005). "Effect of antibiotics on Oxalobacter formigenes colonization of human gastrointestinal tract". Journal of Endourology.
35. (April 2003). "Intestinal Oxalobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate". Journal of Endourology.
36. (June 2008). "Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones". Journal of the American Society of Nephrology.
37. (November 2018). "16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones". Urolithiasis.
38. (December 2018). "Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers". Gut.
39. (July 2019). "Gut microbiome and kidney stone disease: not just an Oxalobacter story". Kidney International.
40. (July 2019). "Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis". Kidney International.
41. (August 2017). "Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project". Microbiome.
42. (March 2017). "''Oxalobacter formigenes-''Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells". Journal of the American Society of Nephrology.
43. (February 2006). "Oxalobacter sp. reduces urinary oxalate excretion by promoting enteric oxalate secretion". Kidney International.
44. (July 2023). "Sel1-like proteins and peptides are the major ''Oxalobacter formigenes''-derived factors stimulating oxalate transport by human intestinal epithelial cells". American Journal of Physiology. Cell Physiology.
45. (November 2011). "Efficacy and safety of Oxalobacter formigenes to reduce urinary oxalate in primary hyperoxaluria". Nephrology, Dialysis, Transplantation.
46. (May 2017). "A randomised Phase I/II trial to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria". Pediatric Nephrology.
47. (August 2018). "A randomised Phase II/III study to evaluate the efficacy and safety of orally administered Oxalobacter formigenes to treat primary hyperoxaluria". Urolithiasis.
48. (2021-07-23). "Effects of Oxalobacter formigenes in subjects with primary hyperoxaluria Type 1 and end-stage renal disease: a Phase II study". Nephrology Dialysis Transplantation.
49. (February 2023). "ePHex: a phase 3, double-blind, placebo-controlled, randomized study to evaluate long-term efficacy and safety of Oxalobacter formigenes in patients with primary hyperoxaluria". Pediatric Nephrology.