Direct quantification of the enteric bacterium Oxalobacter formigenes in human fecal samples by quantitative competitive-template PCR

Effects of wheat bran replacement with pomegranate seed pulp on rumen fermentation, gas production, methanogen and protozoa populations of camel and goat rumen using competitive PCR technique: An in vitro study

BACKGROUND

Microbial populations in the rumen play an essential role in the degradation of Cellulosic dietary components and in providing nutrients to the host animal.

OBJECTIVE

This study aims to detect the effect of pomegranate seed pulp (PSP) on rumen fermentation, digestibility and methanogens and the protozoa population (by competitive polymerase chain reaction [PCR]) of the camel and goat rumen fluid.

MATERIALS AND METHODS

PSP was added to the experimental treatments and replaced by wheat bran (0%, 5% and 10%). Rumen fluid was collected from three goats and two camels according to the similarity of sex, breed, origin and time and used for three gas production studies. DNA extraction was performed by the RBB + c method, the ImageJ programme calculated band intensities (target and competing DNA), and line gradients were plotted based on the number of copies and intensity.

RESULTS

Our result showed that diets did not significantly affect the methanogen and protozoa population. Animal species affected microbial populations so that both populations in camels were less than goats. The production of gas and volatile fatty acids was not affected by diets. These two parameters and NH3 concentration and methane production in goats were higher than in camel. The pH of digested dry matter and microbial protein in camels was higher than in goats.

CONCLUSIONS

Therefore, the competitive PCR technique is an effective method for enumerating rumen microbiota. This supplementation can be considered a strategy to achieve performance and environmental benefits.

Oxalobacter formigenes reduce the risk of kidney stones in patients exposed to oral antibiotics: a case-control study

This is the first prospective study to investigate the association between kidney stones, bone mineral density, serum testosterone, colon cancer and O. formigenes colonization. 40 kidney stone patients and 85 controls were enrolled. O. formigenes colonization was established. BMD was examined from T- and Z-scores using dual energy absorptiometry. O. formigenes was found in 28 of 40 cases and 80 of 85 controls. BMD was significantly reduced in patients (p < 0.05). The evaluation revealed a significant association between lowered O. formigenes colonization and low testosterone. Urinary calcium and oxalates levels were greater in patient. Serum testosterone and urinary citrate concentrations was reduced in patients with a significant difference. Also an association between O. formigenes and colon cancer was noted. Absence of O. formigenes might stand for a pathogenic factor in calcium oxalate stone, low bone mineral density, low testosterone levels and also colon cancer, when antibiotics are prescribed generously.

Calcium Oxalate Nephrolithiasis and Gut Microbiota: Not just a Gut-Kidney Axis. A Nutritional Perspective

Recent studies have shown that patients with kidney stone disease, and particularly calcium oxalate nephrolithiasis, exhibit dysbiosis in their fecal and urinary microbiota compared with controls. The alterations of microbiota go far beyond the simple presence and representation of Oxalobacter formigenes, a well-known symbiont exhibiting a marked capacity of degrading dietary oxalate and stimulating oxalate secretion by the gut mucosa. Thus, alterations of the intestinal microbiota may be involved in the pathophysiology of calcium kidney stones. However, the role of nutrition in this gut-kidney axis is still unknown, even if nutritional imbalances, such as poor hydration, high salt, and animal protein intake and reduced fruit and vegetable intake, are well-known risk factors for kidney stones. In this narrative review, we provide an overview of the gut-kidney axis in nephrolithiasis from a nutritional perspective, summarizing the evidence supporting the role of nutrition in the modulation of microbiota composition, and their relevance for the modulation of lithogenic risk.

Oxalate-degrading bacteria, including Oxalobacter formigenes, colonise the gastrointestinal tract of healthy koalas (Phascolarctos cinereus) and those with oxalate nephrosis

BACKGROUND

Koalas in the Mount Lofty Ranges, South Australia, have a high prevalence of oxalate nephrosis, or calcium oxalate kidney crystals. Gastrointestinal tract oxalate-degrading bacteria, particularly Oxalobacter formigenes, have been identified in other animal species and humans, and their absence or low abundance is postulated to increase the risk of renal oxalate diseases. This study aimed to identify oxalate-degrading bacteria in the gastrointestinal tract of koalas and determine their association with oxalate nephrosis.

METHODS

Caecal and faecal samples were collected at necropsy from 22 Mount Lofty Ranges koalas that had been euthanased on welfare grounds, with 8 koalas found to have oxalate nephrosis by renal histopathology. Samples were analysed by PCR for the oxc gene, which encodes oxalyl-CoA decarboxylase, and also by Illumina sequencing of the V3-V4 region of the bacterial 16S rRNA gene.

RESULTS

The oxc gene was detected in 100% of koala samples, regardless of oxalate nephrosis status. Oxalobacter formigenes was detected in all but one faecal sample, with no difference in abundance between koalas affected and unaffected by oxalate nephrosis. Other species of known oxalate-degrading bacteria were infrequently detected.

CONCLUSION

This is the first study to identify Oxalobacter and other oxalate-degrading bacterial species in koalas, but an association with oxalate nephrosis and absence or low abundance of Oxalobacter was not found. This suggests other mechanisms underlie the risk of oxalate nephrosis in koalas.

The role of the microbiome in kidney stone formation

Nephrolithiasis is a complex disease of worldwide prevalence that is influenced by both genetic and environmental factors. About 75% of kidney stones are predominantly composed of calcium oxalate and urinary oxalate is considered a crucial risk factor. Microorganisms may have a role in the pathogenesis and prevention of kidney stones and the involvement of the intestinal microbiome in this renal disease has been a recent area of interest. Oxalobacter formigenes is a gram negative bacteria that degrades oxalate in the gut decreasing urinary oxalate excretion. In this review, we examine the data studying the role of Oxalobacter formigenes in kidney stone disease in humans and animals, the effect of antibiotics on its colonization, and the potential role of probiotics and whole microbial communities as therapeutic interventions.

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation

Gut microbes are essential for the degradation of dietary oxalate, and this function may play a role in decreasing the incidence of kidney stones. However, many oxalate-degrading bacteria are susceptible to antibiotics and the use of oxalate-degrading probiotics has only led to an ephemeral reduction in urinary oxalate. The objective of the current study was to determine the efficacy of using whole-community microbial transplants from a wild mammalian herbivore, Neotoma albigula, to increase oxalate degradation over the long term in the laboratory rat, Rattus norvegicus. We quantified the change in total oxalate degradation in lab rats immediately after microbial transplants and at 2- and 9-month intervals following microbial transplants. Additionally, we tracked the fecal microbiota of the lab rats, with and without microbial transplants, using high-throughput Illumina sequencing of a hyper-variable region of the 16S rRNA gene. Microbial transplants resulted in a significant increase in oxalate degradation, an effect that persisted 9 months after the initial transplants. Functional persistence was corroborated by the transfer, and persistence of a group of bacteria previously correlated with oxalate consumption in N. albigula, including an anaerobic bacterium from the genus Oxalobacter known for its ability to use oxalate as a sole carbon source. The results of this study indicate that whole-community microbial transplants are an effective means for the persistent colonization of oxalate-degrading bacteria in the mammalian gut.

The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults

PURPOSE

Oxalobacter formigenes, a member of the human colonic microbiota with a major role in net colonic oxalate transport and secretion, is protective against the formation of calcium oxalate kidney stones. We describe the prevalence, relative abundance and stability of O. formigenes in healthy young adults in the United States.

MATERIALS AND METHODS

We used HMP (Human Microbiome Project) data on fecal samples from 242 healthy young adults who had 1 to 3 study visits. Samples underwent whole genomic shotgun sequencing and/or 16S rRNA sequencing. Three data sets available from the processed sequence data were studied, including whole genomic shotgun metagenomic analysis by alignment to reference genomes using shotgun community profiling, or MetaPhlAn (http://huttenhower.sph.harvard.edu/metaphlan) or QIIME (http://qiime.org/) analysis of the V1-3 or V3-5 16S sequences.

RESULTS

O. formigenes was detected in fecal samples using whole genomic shotgun and 16S rRNA data. Analysis of the whole genomic shotgun data set using shotgun community profiling showed that 29 of 94 subjects (31%) were O. formigenes positive. V1-3 and V3-5 analyses were less sensitive for O. formigenes detection. When present, O. formigenes relative abundance varied over 3 log10 and was normally distributed. All assays agreed in 58 of 66 samples (88%) studied by all 3 methods. Of 14 subjects who were O. formigenes positive at baseline 13 (93%) were positive at the followup visit, indicating the stability of colonization.

CONCLUSIONS

O. formigenes appears to be stably present in fewer than half of healthy young adults in the United States. It is most sensitively detected by whole genomic shotgun.

Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group

AIM

To examine whether enhanced diversity or numbers of oxalate-degrading bacteria in the gastrointestinal tracts of black South Africans play a role in determining the rarity of urolithiasis in this group.

METHODS AND RESULTS

Fresh faecal samples collected from healthy black and white South African male volunteers were analysed in terms of bacterial oxalate-degrading activity, bacterial diversity and relative species abundance. Varied bacterial populations prepared from samples from the low-risk black group showed a significantly higher level of oxalate degradation. Denaturing gradient gel electrophoresis analyses of Lactobacillus and related spp. and Bifidobacterium spp. 16S rRNA PCR products revealed a significantly higher faecal Lactobacillus diversity for the low-risk black group relative to the higher-risk white group. Quantitative real-time PCR experiments did not show any significant differences between the study groups for Lactobacillus and related spp.. However, Bifidobacterium spp. were present at a significantly higher relative abundance in the black group. Oxalobacter formigenes was present only at very low levels in either group.

CONCLUSIONS

The low abundance of O. formigenes and increased diversity and abundance of oxalate-degrading Lactobacillus and Bifidobacterium spp. in the black South African population suggest that these strains rather than O. formigenes may protect this group against calcium oxalate kidney stone disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

The South African black population harbours a pool of potential oxalate-degrading lactic acid bacteria, which is more abundant and diverse than that of white South Africans. This may be useful in developing probiotics for calcium oxalate kidney stone prophylaxis.

Quantitative analysis of colonization with real-time PCR to identify the role of Oxalobacter formigenes in calcium oxalate urolithiasis

The objective of the study was to quantitatively measure the number of Oxalobacter formigenes (O. formigenes) colonizations in the gastrointestinal tract in calcium oxalate-forming patients with real-time polymerase chain reaction (PCR). Calcium oxalate-forming patients (n: 27) were included in the study. Serum calcium, sodium, potassium, urea and creatinine levels, as well as 24 h urine levels of calcium and oxalate were measured. The numbers of O. formigenes colonies in stool samples were detected by real-time PCR. One or two metabolic abnormalities were detected in 15 of 27 patients. The O. formigenes levels in patients with metabolic disturbance were significantly decreased when compared to the patients with no metabolic abnormalities (p: 0.038). The undetectable levels of O. formigenes were encountered in one of five patients with hypercalciuria, in three of four patients with hyperoxaluria and in four of six patients with both hypercalciuria and hyperoxaluria. In nine patients with a history of stone recurrence, O. formigenes colonization was significantly lower than the patients with the first stone attack (p: 0.001). O. formigenes formation ceased or significantly diminished in patients with calcium oxalate stones with a coexistence of both hyperoxaluria and hypercalciuria. The measurement of O. formigenes colonies by real-time PCR seemed to be an inconvenient and expensive method. For this reason, the real-time PCR measurements can be spared for the patients with stone recurrences and with metabolic abnormalities like hypercalciuria and hyperoxaluria. The exact measurement of O. formigenes may also help more accurate programming of O. formigenes-based treatments.

Case report of paediatric oxalate urolithiasis and a review of enteric hyperoxaluria

The formation of renal calculi secondary to enteric hyperoxaluria is rare in the paediatric population. We present the case of an 8-year-old boy who had short bowel syndrome resulting in enteric hyperoxaluria which led to the development of urolithiasis and bilateral ureteric strictures, both of which resolved with medical management. We also review the literature on enteric hyperoxaluria.

Intestinal colonization with Oxalobacter formigenes and its relation to urinary oxalate excretion in pediatric patients with idiopathic calcium urolithiasis

BACKGROUND AND AIM

Oxalobacter formigenes is an intestinal bacterium that utilizes oxalate as the only source of energy. It has been suggested that the lack of colonization with this organism may be a risk factor for calcium oxalate urolithiasis. Because this problem was not investigated in pediatric stone formers, we decided to assess it in our patients.

METHODS

The presence of O. formigenes in stool samples of 76 children and adolescents (aged 4.1-18 years) with idiopathic calcium urolithiasis (36 with chemically confirmed calcium oxalate stones and 40 children with a strong clinical suspicion of this type of urolithiasis) was assessed using PCR method. Simultaneously, urinary oxalate excretion was measured in this group. Fifty healthy, age- and sex-matched subjects served as controls.

RESULTS

O. formigenes was found in 21/76 patients (27.6%). In controls, frequency of colonization was similar (26%). The median 24h urinary oxalate excretion in patients colonized with O. formigenes was significantly lower in comparison with non-colonized patients, 0.319 (range 0.141-0.546) and 0.437 (range 0.198-0.967) mmol/1.73 m(2)/24h, respectively.

CONCLUSIONS

Higher urinary oxalate excretion in children with calcium urolithiasis may be a result of the absence of O. formigenes. The reasons for similarly low intestinal colonization with this bacterium in normal subjects and stone formers remain speculative. Thus, further studies are necessary to clarify this issue.

Variability of Oxalobacter formigenes and oxalate in stool samples

PURPOSE

The intestinal organism Oxalobacter formigenes is unique in using oxalate as its primary carbon and energy source. Intestinal colonization with O. formigenes may have clinical significance by decreasing intestinal oxalate and its absorption, thereby influencing the concentration of oxalate in plasma and urine, and the development of calcium oxalate stone disease. Because the oxalate content of the diet varies considerably, we hypothesized that the number of O. formigenes and amount of oxalate would vary in feces.

MATERIALS AND METHODS

To enumerate the number of O. formigenes in feces an accurate and reproducible real-time polymerase chain reaction assay was developed to quantify O. formigenes DNA. Stool samples were obtained from 10 colonized individuals to determine the levels of O. formigenes by this assay and the oxalate content by ion chromatography.

RESULTS

Concentrations of O. formigenes ranged from lower than the limit of detection of 5 x 10(3) to 1.04 x 10(9) cells per gm stool. The total oxalate content of stool samples varied from 0.1 to 1.8 mg/gm and fecal water oxalate varied from 60 to 600 microM. All parameters measured varied within each stool collection, among stool collections on different days and among individuals. Notably in 7 of 10 individuals at least 1 stool sample contained no detectable O. formigenes. In addition, 7 of 10 subjects had a fecal colonization of less than 4 x 10(4) per gm stool.

CONCLUSIONS

This study demonstrates that there is intrastool and interstool sample variability in the amount of O. formigenes measured by real-time polymerase chain reaction that did not correlate with the quantity of oxalate in stool. Most subjects had a fecal colonization of less than 4 x 10(4) per gm stool.

Oxalate degrading bacteria: new treatment option for patients with primary and secondary hyperoxaluria?

Current treatment options in patients with primary and secondary hyperoxaluria are limited and do not always lead to sufficient reduction in urinary oxalate excretion. Intestinal oxalate degrading bacteria are capable of degrading oxalate to CO(2) and formate, the latter being further metabolized and excreted via the feces. It is speculated, that both endogenously produced, as well as dietary oxalate can be significantly removed via the intestinal tract. Oxalobacter formigenes, an obligate anaerobic microbe normally found in the intestinal tract has one oxalate degrading enzyme, oxalyl-CoA decarboxylase, which is also found in Bifidobacterium lactis. Other bacteria with possible oxalate degrading potency are lactic acid bacteria, as well as Enterococcus faecalis and Eubacterium lentum. However, specific therapeutic studies on humans are scarce and, except for Oxalobacter, data are not congruent. We found the oral application of Oxalobacter successful in patients with primary hyperoxaluria. However, long-term post-treatment follow-up of 1-2 years showed that constant intestinal colonization is not achieved in most patients. In one patient with constant colonization, urinary oxalate excretion normalized over time. Short-term studies with other bacteria such as lactic acid bacteria did not show a specific reduction in urinary oxalate excretion. O. formigenes might be a promising new therapeutic tool in patients with primary and secondary hyperoxaluria.

Absorptive hyperoxaluria leads to an increased risk for urolithiasis or nephrocalcinosis in cystic fibrosis

BACKGROUND

Hyperoxaluria has been incriminated to account for the increased incidence of urolithiasis or nephrocalcinosis in patients with cystic fibrosis (CF). Hyperoxaluria presumably is caused by fat malabsorption and the absence of such intestinal oxalate-degrading bacteria as Oxalobacter formigenes. To better elucidate its pathophysiological characteristics, we prospectively studied patients with CF by determining these parameters and performing renal ultrasonography twice yearly.

METHODS

In addition to routine tests in urine (lithogenic and stone-inhibitory substances), the presence of O formigenes was tested in stool, plasma oxalate was measured, and a [13C2]oxalate absorption test was performed in 37 patients with CF aged 5 to 37 years (15 females, 22 males) who were constantly hyperoxaluric before the study.

RESULTS

Hyperoxaluria (oxalate, 46 to 141 mg/1.73 m2/24 h [0.51 to 1.57 mmol/1.73 m2/24 h]; normal, < 45 mg/1.73 m2/24 h [< 0.5 mmol/1.73 m2/24 h]) was now found in 24 patients (64.8%). Plasma oxalate levels were elevated in 6 patients (7.92 to 19.5 micromol/L; normal, 6.3 +/- 1.1 micromol/L). Oxalobacter species were detected in only 1 patient. Intestinal oxalate absorption was elevated (11.4% to 28.5%; normal, < 10%) in 23 patients. Hypocitraturia was present in 17 patients (citrate, 0.35 to 2.8 g/1.73 m2/24 h [0.2 to 1.1 mmol/1.73 m2/24 h]; normal female, > 2.8 mg/1.73 m2/24 h [> 1.6 mmol/1.73 m2/24 h]; male, > 3.3 mg/1.73 m2/24 h [> 1.9 mmol/1.73 m2/24 h]). Urine calcium oxalate saturation was elevated in 17 patients (5.62 to 28.9 relative units; normal female, < 5.5 relative units; male, < 6.3 relative units). In 16% of patients, urolithiasis (n = 2) or nephrocalcinosis (n = 4) was diagnosed ultrasonographically.

CONCLUSION

Absorptive hyperoxaluria and hypocitraturia are the main culprits for the increased incidence of urolithiasis and nephrocalcinosis in patients with CF. We advocate high fluid intake, low-oxalate/high-calcium diet, and alkali citrate medication, if necessary. Additional studies are necessary to determine the influence of Oxalobacter species or other oxalate-degrading bacteria on oxalate handling in patients with CF.

Effect of antibiotics on Oxalobacter formigenes colonization of human gastrointestinal tract

BACKGROUND AND PURPOSE

Oxalobacter formigenes is a bacterium residing in the human gastrointestinal tract that degrades oxalate and reduces its availability for absorption. This bacterium is assumed to be antibiotic sensitive, and repeated antibiotic therapies could eradicate it. The aim of the present study was to determine the differences in the colonization by O. formigenes of individuals who had been on antibiotics for at least 5 days at the time of sample collection and individuals who had not taken antibiotics for at least 3 months.

PATIENTS AND METHODS

Stool samples were collected from 80 individuals without stone disease (35 with and 45 without antibiotic consumption) and 100 patients with stone disease (20 with and 80 without antibiotic consumption). Oxalobacter formigenes was detected by a polymerase chain reaction-based method, and the presence/absence of O. formigenes was correlated with urinary oxalate concentrations.

RESULTS

Lower percentages of individuals without stone disease and with stone disease who were consuming antibiotics had O. formigenes colonization than individuals without antibiotic consumption. Urinary oxalate concentrations were higher in the individuals without O. formigenes than in colonized individuals.

CONCLUSION

Our observations confirm a direct association between antibiotic consumption and absence of O. formigenes. Absence of intestinal O. formigenes could represent a pathogenic factor in calcium oxalate urolithiasis when antibiotics are prescribed generously.

URINARY TRACT BIOMATERIALS

PURPOSE

As a result of endourological advances, biomaterials have become increasingly used within the urinary tract. This review article provides an update on the current status of urinary tract biomaterials, discussing issues of biocompatibility, biomaterials available for use, clinical applications and biomaterial related complications. Perspectives on future materials for use in the urinary tract are also provided.

MATERIALS AND METHODS

We performed a comprehensive search of the peer reviewed literature on all aspects of biomaterials in the urinary tract using PubMed and MEDLINE. All pertinent articles were reviewed in detail.

RESULTS

Any potential biomaterial must undergo rigorous physical and biocompatibility testing prior to its commercialization and use in humans. There are currently many different bulk materials and coatings available for the manufacturing of biomaterials, although the ideal material has yet to be discovered. For use in the urinary tract, biomaterials may be formed into devices, including ureteral and urethral stents, urethral catheters and percutaneous nephrostomy tubes. Despite significant advances in basic science research involving biocompatibility issues and biofilm formation, infection and encrustation remain associated with the use of biomaterials in the urinary tract and, therefore, limit their long-term indwelling time.

CONCLUSIONS

Prosthetic devices formed from biomaterials will continue to be an essential tool in the practicing urologist's armamentarium. Ongoing research is essential to optimize biocompatibility and decrease biomaterial related complications such as infection and encrustation within the urinary tract. Future advances include biodegradables, novel coatings and tissue engineering.

Oxalobacter formigenes and its role in oxalate metabolism in the human gut

Oxalate is ingested in a wide range of animal feeds and human foods and beverages and is formed endogenously as a waste product of metabolism. Bacterial, rather than host, enzymes are required for the intestinal degradation of oxalate in man and mammals. The bacterium primarily responsible is the strict anaerobe Oxalobacter formigenes. In humans, this organism is found in the colon. O. formigenes has an obligate requirement for oxalate as a source of energy and cell carbon. In O. formigenes, the proton motive force for energy conservation is generated by the electrogenic antiport of oxalate(2-) and formate(1-) by the oxalate-formate exchanger, OxlT. The coupling of oxalate-formate exchange to the reductive decarboxylation of oxalyl CoA forms an 'indirect' proton pump. Oxalate is voided in the urine and the loss of O. formigenes may be accompanied by elevated concentrations of urinary oxalate, increasing the risk of recurrent calcium oxalate kidney stone formation. Links between the occurrence of nephrolithiasis and the presence of Oxalobacter have led to the suggestion that antibiotic therapy may contribute to the loss of this organism from the colonic microbiota. Studies in animals and human volunteers have indicated that, when administered therapeutically, O. formigenes can establish in the gut and reduce the urinary oxalate concentration following an oxalate load, hence reducing the likely incidence of calcium oxalate kidney stone formation. The findings to date suggest that anaerobic, colonic bacteria such as O. formigenes, that are able to degrade toxic compounds in the gut, may, in future, find application for therapeutic use, with substantial benefit for human health and well-being.

Ureteric stenting 25 years on: routine or risky?

BACKGROUND

Ureteric stents have been used in urological practice for over 25 years and in many cases have become almost routine. The purpose of the present review is to highlight the uses, complications and risk management issues associated with their use.

METHODS

An extensive literature review was conducted and knowledge from past experience was accessed to give a summary of past and current ureteric stent use in urology.

RESULTS

Broadly, there are stone and non-stone indications for stenting. Complications may range from the commonly experienced 'stent syndrome' to the medico-legal dilemma of the forgotten stent. Risk management must be applied to all uses of stenting to minimize complications and achieve best practice.

CONCLUSION

Although almost routine in many areas of urological practice, the complications and implications for risk management of ureteric stenting cannot be ignored.

Urinary oxalate levels and the enteric bacterium Oxalobacter formigenes in patients with calcium oxalate urolithiasis

OBJECTIVES

We performed a prospective study to evaluate the intestinal colonization of Oxalobacter formigenes and its relationship with urinary oxalate levels in patients with calcium oxalate stone disease.

METHODS

One hundred and three patients with calcium oxalate urolithiasis, ranging in age from 21 to 73 years (mean age, 47 years) who were followed from August 2000 to September 2001 participated in this study. Fresh stool and 24-hour urine samples were collected. Genus specific oligonucleotide sequences corresponding to the homologous regions residing in the oxc gene were designed. In order to quantify O. formigenes in clinical specimens, a quantitative-PCR-based assay system utilizing a competitive DNA template as an internal standard was developed. Urine volume, pH, creatinine, oxalate, calcium, magnesium, phosphate, citrate and uric acid were measured.

RESULTS

Intestinal Oxalobacteria were detected in 45.6% (n=47) of calcium oxalate stone patients by PCR. In stone formers who tested negative for Oxalobacteria, the average urinary oxalate level was 0.36 mmol/day, and this compared to 0.29 mmol/day for those patients that tested positive for Oxalobacteria (p<0.05). Mean colony forming units per gram of stool of all patients was 1.1 x 10(7) (0-4.1 x 10(8)), and the level of 24 hours urine oxalate significantly decreased with increasing level of colony forming units of O. formigenes (r=-0.356, p=0.021).

CONCLUSION

Our results support the concept that O. formigenes is important in maintaining oxalate homeostasis and that its absence from the gut may be the risk of calcium oxalate urolithiasis.

Microorganisms and Calcium Oxalate Stone Disease

Microorganisms may have a role in the pathogenesis and prevention of kidney stones. The subjects of this review include nanobacteria, Oxalobacter formigenes, and lactic acid bacteria. Not reviewed here is the well-described role of infections of the urinary tract with Proteus species and other urease-producing organisms associated with struvite stone formation. Nanobacteria have been proposed to be very small (0.08-0.5 nm), ubiquitous organisms that could play a role in stone formation. The theory is that nanobacteria can nucleate carbonate apatite on their surfaces and thereby provide the nidus for stone formation. However, their existence remains uncertain and many investigators are openly skeptical. Recent investigations suggest that they are artifacts, and not actually living organisms, but their proponents continue to study them. O. formigenes is an obligate anaerobe which may be important in the prevention of stone formation. Its sole substrate for generation of ATP is oxalate. It may thereby metabolize its human host's dietary oxalate and diminish intestinal absorption and subsequent urinary excretion of oxalate. There is evidence that the organism's absence, perhaps sometimes due to courses of antibiotics, may be a cause of hyperoxaluria and stone formation. In early investigations, patients not colonized with the organism can be recolonized. Urinary oxalate can be diminished by accompanying an oxalate-containing meal with the organism. One study demonstrated that a preparation of lactic acid bacteria successfully reduced urinary oxalate excretion in 6 patients with calcium oxalate stones and hyperoxaluria. The mechanism of this effect is uncertain since these bacteria lacked the gene possessed by O. formigenes which codes for that organism's oxalate uptake mechanism. The author is currently completing a small randomized controlled clinical trial with this preparation in calcium stone-forming patients with idiopathic hyperoxaluria.

The association of nephrolithiasis with cystic fibrosis

BACKGROUND

There is a growing body of evidence regarding the association between cystic fibrosis (CF) and nephrolithiasis and the role that Oxalobacter formigenes may have in that association.

METHODS

We performed a MEDLINE search of "cystic fibrosis and nephrolithiasis" and "Oxalobacter formigenes." Epidemiological and experimental evidence and possible mechanisms explaining the association were critically reviewed.

RESULTS

Of patients with CF, 3.0% to 6.3% are affected with nephrolithiasis, a percentage greater than that of age-matched controls without CF, in whom the rate is 1% to 2%. Studies have suggested possible mechanisms for the association, including hyperuricosuria, hyperoxaluria, primary defects in calcium handling caused by mutation of the CF transmembrane regulator (CFTR), hypocitraturia, and lack of colonization with O formigenes, an enteric oxalate-degrading bacterium. The absence of colonization could be related to frequent courses of antibiotics.

CONCLUSION

Although the incidence of stones in patients with CF may be increased compared with controls without CF, many possible mechanisms are implicated. The relative contributions of these mechanisms remain uncertain. Future directions may include specific identification of lithogenic risks and therapy aimed at stone prevention in this population.

Oxalate-degrading enzymes from Oxalobacter formigenes: a novel device coating to reduce urinary tract biomaterial-related encrustation

BACKGROUND AND PURPOSE

The long-term placement of biomaterials within the urinary tract is limited by the development of encrustation. In a noninfected urinary environment, encrustation often results from the deposition of calcium oxalate on the biomaterial surface. There is an association between the absence of Oxalobacter formigenes, a commensal colonic bacterium capable of degrading oxalate, and calcium oxalate stone formation. This pilot study was designed to evaluate several oxalate-degrading enzymes produced by O. formigenes as a potential biomaterial coating to reduce urinary tract encrustation.

MATERIALS AND METHODS

Circular silicone disks of 6-mm diameter were incubated for 48 hours in oxalylcoenzyme A decarboxylase (OXC), formyl-coenzyme A transferase (FRC), and coenzyme A, while control disks were incubated in distilled water. The adsorption of OXC and FRC was assessed using enhanced chemiluminescence (ECL) and atomic force microscopy (AFM). Coated and uncoated disks (20 of each) were implanted in the bladders of 40 female New Zealand White rabbits. After 30 days, the disks were recovered, and the degree of encrustation on the polymer surface was evaluated utilizing dry weight measurement, calcium atomic absorption spectroscopy (AAS), and scanning electron microscopy/energy-dispersive X-ray analysis (SEM/EDX).

RESULTS

Both ECL and AFM demonstrated coating of the silicone disks with OXC and FRC. The mean dry weights of the coated and control disks following explantation were 0.591 +/- 0.438 g and 0.747 +/- 0.428 g, respectively (P = 0.307). The mean weight of calcium on the coated and control disks, as determined by AAS, was 154.1 +/- 96.25 mg and 258 +/- 181.35 mg, respectively (P = 0.008).

CONCLUSIONS

The use of oxalate-degrading enzymes from O. formigenes to coat urinary biomaterials represents a novel paradigm to reduce biomaterial-related encrustation. Coating of silicone with oxalate-degrading enzymes from O. formigenes results in a modest reduction in encrustation with no apparent toxicity. Further studies are warranted.

Molecular epidemiology of fecal Oxalobacter formigenes in healthy adults living in Seoul, Korea

BACKGROUND AND PURPOSE

Oxalobacter formigenes is a member of the intestinal flora that degrades oxalate. This bacterium maintains an important symbiotic relation with its hosts by regulating oxalic acid absorption in the intestine as well as oxalic acid concentrations in plasma. We tried to define the prevalence of fecal O. formigenes positivity in healthy adults.

MATERIALS AND METHODS

Whole-bacterial DNA was isolated directly from fresh stool samples obtained from 233 healthy adults known to be free of urolithiasis. Genus-specific oligonucleotide sequences corresponding to homologous regions residing in the oxc gene that encodes oxalyl-coenzyme A decarboxylase were designed. A PCR-based assay was done on the stool samples.

RESULTS

A PCR product of 416 bp encoding the oxc gene was detected in 197 of the 233 stool samples (76.8%). Adjusted to the Seoul population census 1995, the calibrated fecal O. formigenes-positive rate was estimated to be 76.7%: 79.2% in men and 74.2% in women, with no significance difference according to age or sex.

CONCLUSION

These results suggest that O. formigenes inhabits the intestine of three fourths of the normal Korean populations. These data provide a base for further studies to uncover the relation between O. formigenes and urolithiasis.

Intestinal Oxalobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate

BACKGROUND AND PURPOSE

Oxalobacter formigenes is an anaerobic commensal colonic bacterium capable of degrading oxalate through the enzyme oxalyl-CoA decarboxylase. It has been theorized that individuals who lack this bacterium have higher intestinal oxalate absorption, leading to a higher urinary oxalate concentration and an increased risk of calcium oxalate urolithiasis. We performed a prospective, controlled study to evaluate O. formigenes colonization in calcium oxalate stone formers and to correlate colonization with urinary oxalate and other standard urinary stone risk factors.

PATIENTS AND METHODS

Thirty-five first-time calcium oxalate stone formers were compared with 10 control subjects having no history of urolithiasis and a normal renal ultrasound scan. All subjects underwent standard metabolic testing by submitting serum and 24-hour urine specimens. In addition, all subjects submitted stool samples for culture and detection of O. formigenes by Xentr(ix) O. formigenes Monitor.

RESULTS

Intestinal Oxalobacter was detected in only 26% of the stone formers compared with 60% of the controls (p < 0.05). Overall, the average urinary oxalate excretion by the two groups was similar (38.6 mg/day v 40.8 mg/day). Among stone formers, however, there were statistically higher urinary oxalate concentrations in O. formigenes-negative patients compared with those testing positive (41.7 mg/day v 29.4 mg/day) (p = 0.03). Furthermore, all 10 stone formers with hyperoxaluria (>44 mg/day) tested negative for O. formigenes (p < 0.05).

CONCLUSIONS

Calcium oxalate stone formers have a low rate of colonization with O. formigenes. Among stone formers, absence of intestinal Oxalobacter correlates with higher urinary oxalate concentration and an increased risk of hyperoxaluria. Introduction of the Oxalobacter bacterium or an analog of its enzyme oxalyl-CoA decarboxylase into the intestinal tract may be a treatment for calcium oxalate stone disease.

Tips and tricks for the management of retained ureteral stents

BACKGROUND AND PURPOSE

Retained ureteral stents, especially those that are encrusted and associated with a stone burden, can be a difficult management problem. We review our experience and the different options employed for treating this complication.

PATIENTS AND METHODS

From July 1998 to February 2002, 26 retained ureteral stents were managed in our department. The average patient age was 45.9 years (range 8-77 years). The average time the stent had been in place was 10.7 months (range 3-28 months). Prior to planning definitive therapy, a plain radiograph with tomographic views was reviewed.

RESULTS

A guidewire or Glidewire was often placed adjacent to the stent in order to maintain ureteral access and in some cases was able to facilitate removal of the retained stent. The patients required an average of 2.7 endourologic procedures (range 1-4) performed at one or more sessions to remove the stent and all associated stone burden. If the stone burden could not be entirely removed then stent extraction and subsequent sessions were performed until stone-free status was achieved. Cystolitholapaxy was required to treat the distal component of stent encrustation in 20 cases. Percutaneous nephrolithotomy was performed in four patients, antegrade ureteroscopy with or without intracorporeal lithotripsy in four patients, retrograde ureteroscopy with or without laser lithotripsy in five patients, and extracorporeal shockwave lithotripsy in seven patients to treat the proximal component of stent encrustation. The stent could be removed in a single anesthetic session in 23 of 26 cases (88.5%). Analysis revealed that the major component of the encrustations was a combination of calcium oxalate and phosphate.

CONCLUSION

Successful management of retained ureteral stents requires careful planning and may entail a combination of endourologic approaches. It is imperative to avoid using significant force, which can result in severe ureteral injury or breakage of the stent. If encrustations are present along the stent, we believe in treating the distal component prior to managing any proximal or ureteral components.

Hyperoxaluric calcium nephrolithiasis

Hyperoxaluria leads to increased calcium oxalate supersaturation and calcium oxalate stone formation. Excess oxalate can arise from endogenous overproduction as in primary hyperoxaluria or from dietary sources. In the last 15 years great strides have been made in the diagnosis and treatment of primary hyperoxaluria. However options still seem limited in treating the mild hyperoxaluria found in many stone formers. Inadequate knowledge of food oxalate content, the effect of dietary oxalate precursors on oxalate excretion, and the factors affecting handling of oxalate by the intestine prevent development of rational therapies for treatment of hyperoxaluria. Recent studies of oxalate degrading bacteria and renewed interest in the role of diet calcium in oxalate absorption may lead to better therapeutic strategies for hyperoxaluric calcium nephrolithiasis.

Role of Oxalobacter formigenes in calcium oxalate stone disease: a study from North India

OBJECTIVE

The present study was performed to detect the presence of an oxalate degrading bacteria Oxalobacter formigenes in the GI tract of calcium oxalate stone patients and normal individuals from North India. Furthermore, the possible relationship of this bacterium with number of stone episodes in this part of the world was also studied. The correlation of the presence or absence of O. formigenes with the urinary oxalate levels was evaluated.

METHODS

DNA was extracted from the stool samples of 63 calcium oxalate stone formers and 40 normal individuals. Polymerase chain reaction (PCR) was performed using genus specific primers for O. formigenes. The presence of which was confirmed by Southern blotting. Urinary oxalate levels were tested in each patient.

RESULTS

As shown by PCR and Southern blotting, O. formigenes was present in 65% of normal individuals and in 30% of calcium oxalate stone formers. In patients with three or greater than three stone episodes colonies were present only in 5.6% of patients. Oxalate excretion was less in patients colonized with O. formigenes as compared to those with no colonization.

CONCLUSION

In North Indian population the absence of O. formigenes can lead to a significant increase in the risk of absorptive hyperoxaluria and resultant recurrent calcium oxalate stone episodes.

Rapid reversal of hyperoxaluria in a rat model after probiotic administration of Oxalobacter formigenes

PURPOSE

The gut inhabiting bacterium Oxalobacter formigenes may be a negative risk factor in recurrent calcium oxalate kidney stone disease that apparently maintains oxalic acid homeostasis in its host via the degradation of dietary oxalate. The possibility of using this bacterium as probiotic treatment to reduce urinary oxalate was investigated in a rat model.

MATERIALS AND METHODS

Male Sprague-Dawley rats were placed on a diet supplemented with ammonium oxalate to induce a state of severe hyperoxaluria. Subgroups of these rats received an esophageal gavage of 1 x 10(3), 10(5), 10(7) or 10(9) O. formigenes per feeding for a 2-week period. Each rat was followed for general health and changes in urinary oxalate.

RESULTS

Rats with chronic hyperoxaluria resulting from high dietary oxalate that were treated with O. formigenes showed decreased urinary oxalate within 2 days of initiating probiotic supplementation. The amount of the decrease in a 2-week period proved directly proportional to the dose of bacteria. Urinary oxalate in rats receiving higher amounts of O. formigenes returned to almost normal. Throughout the study the rats remained healthy with no signs of toxicity, antibody development or a histopathological condition.

CONCLUSIONS

Probiotic treatment of hyperoxaluric rats with O. formigenes may significantly and rapidly reduce the level of oxalate in the urine. This probiotic treatment appears to be safe and well tolerated. The approach may be feasible for treating calcium oxalate kidney stone disease.

Molecular identification of Oxalobacter formigenes with the polymerase chain reaction in fresh or frozen fecal samples

OBJECTIVE

To develop a simple and rapid polymerase chain reaction (PCR) method for detecting Oxalobacter formigenes (which degrades oxalate in the gut) in fecal specimens from healthy volunteers and patients with urolithiasis, and to determine whether O. formigenes can be detected in frozen or fresh fecal samples.

MATERIALS AND METHODS

Whole bacterial DNA was isolated directly from fresh and frozen fecal samples obtained from 30 healthy volunteers free from urolithiasis and from fresh fecal samples obtained from 38 patients with urolithiasis. Genus-specific oligonucleotide sequences were designed, corresponding to homologous regions residing in the oxc gene that encodes for oxalyl-coenzyme A decarboxylase. A PCR-based assay was used on both fresh and frozen fecal samples, and the nucleotide sequences analysed to confirm oxc.

RESULTS

A PCR product of 416 bp encoding the oxc gene was detected in 23 (77%) of 30 healthy volunteers free from urolithiasis and in 14 (37%) of 38 patients with urolithiasis. In healthy volunteers, the results of PCR for the fresh and the frozen samples were identical in each subject. The nucleotide sequence analysis showed that the sequence of the amplified product was compatible with that of oxc.

CONCLUSION

O. formigenes can be identified easily and efficiently using this PCR-based detection system. The colonization rate of O. formigenes in patients with urolithiasis was significantly lower than that in healthy volunteers known to be free from urolithiasis. Furthermore, as the PCR-based assay results in the frozen fecal samples were identical to those from fresh samples in each subject, immediate processing of fecal samples may not be necessary to detect O. formigenes in the clinical setting.

Development of a quantitative competitive PCR assay for detection and quantification of Escherichia coli O157:H7 cells

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify Escherichia coli O157:H7 cells. From 10(3) to 10(8) CFU of E. coli O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (r(2) = 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.

Quantitative PCR-ELAHA for the Determination of Retroviral Vector Transduction Efficiency

Current methods to detect transduction efficiency during the routine use of integrating retroviral vectors in gene therapy applications may require the use of radioactivity and usually rely upon subjective determination of the results. We have developed two competitive quantitative assays that use an enzyme-linked, amplicon hybridization assay (ELAHA) to detect the products of PCR-amplified regions of transgene from cells transduced with Moloney murine leukemia virus vectors. The quantitative assays (PCR-ELAHA) proved to be simple, rapid, and sensitive, avoiding the need for Southern hybridization, complex histochemical stains, or often subjective and time-consuming tissue culture and immunofluorescence assays. The PCR-ELAHA systems can rapidly detect proviral DNA from any retroviral vector carrying the common selective and marker genes neomycin phosphotransferase and green fluorescent protein, and the methods described are equally applicable to other sequences of interest, providing a cheaper alternative to the evolving real-time PCR methods. The results revealed the number of copies of retrovector provirus present per stably transduced cell using vectors containing either one or both qPCR targets.

Molecular-phylogenetic analyses of human gastrointestinal microbiota

Molecular-phylogenetic methods have revolutionized the analysis of complex microbial communities. Polymerase chain reaction amplification and phylogenetic analysis of small-subunit ribosomal RNA gene sequences allow microbes to be identified objectively, even in the absence of cultivation. Furthermore, the sequence information obtained by these means can be used to design sequence-based tools for identifying, tracking, and diagnosing the presence of microbes in complex samples. In this article, we summarize this approach and review its application to the study of the human gastrointestinal microbiota. Although just beginning, molecular-phylogenetic surveys of human gut microbes have revealed that most microbes identified in the gastrointestinal tract represent novel, previously undescribed species. A full description of the microbial constituents of the human gut will set the groundwork for interpreting how the gastrointestinal microbiota influence the health of the host.

Encrustation of biomaterials in the urinary tract

The present review focuses on technological advances and relevant research related to encrustation of biomaterials in the urinary tract. The importance of physical and chemical biomaterial type, biocompatibility, material coatings such as hydrogels, and infection related to alloplastic materials used in urological practice are discussed. Recent in-vitro and in-vivo research has focused on materials that will reduce encrustation and bacterial biofilm formation, complications that limit the long-term use of urinary materials. Coordinating scientific resources in a multidisciplinary manner for a better understanding of factors that are involved in encrustation and biofilm formation will offer the potential to modify or resolve the problem of encrustation of foreign materials in the urinary tract.