Oxalate-Degrading Bacteria of the Human Gut as Probiotics in the Management of Kidney Stone Disease. Elsevier; 2010. pp. 63-87. [DOI: 10.1016/s0065-2164(10)72003-7]

The role of intestinal oxalate transport in hyperoxaluria and the formation of kidney stones in animals and man

The intestine exerts a considerable influence over urinary oxalate in two ways, through the absorption of dietary oxalate and by serving as an adaptive extra-renal pathway for elimination of this waste metabolite. Knowledge of the mechanisms responsible for oxalate absorption and secretion by the intestine therefore have significant implications for understanding the etiology of hyperoxaluria, as well as offering potential targets for future treatment strategies for calcium oxalate kidney stone disease. In this review, we present the recent developments and advances in this area over the past 10 years, and put to the test some of the new ideas that have emerged during this time, using human and mouse models. A key focus for our discussion are the membrane-bound anion exchangers, belonging to the SLC26 gene family, some of which have been shown to participate in transcellular oxalate absorption and secretion. This has offered the opportunity to not only examine the roles of these specific transporters, revealing their importance to oxalate homeostasis, but to also probe the relative contributions made by the active transcellular and passive paracellular components of oxalate transport across the intestine. We also discuss some of the various physiological stimuli and signaling pathways which have been suggested to participate in the adaptation and regulation of intestinal oxalate transport. Finally, we offer an update on research into Oxalobacter formigenes, alongside recent investigations of other oxalate-degrading gut bacteria, in both laboratory animals and humans.

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.

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 and ecology of oxalotrophic bacteria

Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.

Primary hyperoxalurias: diagnosis and treatment

Primary hyperoxalurias (PH) comprise a group of three distinct metabolic diseases caused by derangement of glyoxylate metabolism in the liver. Recent years have seen advances in several aspects of PH research. This paper reviews current knowledge of the genetic and biochemical basis of PH, the specific epidemiology and clinical presentation of each type, and therapeutic approaches in different disease stages. Potential future specific therapies are discussed.

Assessment of in vitro oxalate degradation by Lactobacillus species cultured from veterinary probiotics

OBJECTIVE

To culture Lactobacillus spp from veterinary probiotics and measure their in vitro oxalate-degrading capacity.

SAMPLE

2 commercial veterinary probiotics containing Lactobacillus spp.

PROCEDURES

Lactobacillus spp were cultured anaerobically on selective deMan, Rogosa, Sharpe agar medium and subcultured for speciation by 16S rDNA gene sequencing. Isolates were inoculated into broth containing sodium oxalate (5 mg/L) and incubated anaerobically for 72 hours. An oxalate-degrading isolate of Lactobacillus acidophilus (American Type Culture Collection [ATCC] 53544) was the positive control sample; sterile broth containing a known quantity of sodium oxalate was the negative control sample. Oxalate concentrations were detected with ion chromatography. Oxalate degradation was assessed with Dunnett tests to detect differences in mean oxalate concentration for each isolate, compared with results for the negative control.

RESULTS

Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus casei or Lactobacillus zeae (too closely related to differentiate) were isolated from probiotic 1, and L plantarum was isolated from probiotic 2. Sequencing of the 16S rDNA gene confirmed 100% homology to type species. Lactobacillus acidophilus (ATCC 53544) and L acidophilus from probiotic 1 significantly decreased oxalate concentrations by 85.3 and 161.9 mg/L, respectively. Lactobacillus plantarum from probiotics 1 and 2 significantly increased oxalate concentrations by 56.1 and 36.1 mg/L, respectively. Lactobacillus casei did not alter oxalate concentrations.

CONCLUSIONS AND CLINICAL RELEVANCE

Lactobacillus acidophilus isolates significantly reduced oxalate concentrations. In vivo studies are needed to determine whether probiotics containing L acidophilus decrease urine oxalate concentrations and reduce risk of urolith recurrence in dogs with a history of calcium oxalate urolithiasis.

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

Mammalian species have co-evolved with intestinal microbial communities that can shape development and adapt to environmental changes, including antibiotic perturbation or nutrient flux. In humans, especially children, microbiota disruption is common, yet the dynamic microbiome recovery from early-life antibiotics is still uncharacterized. Here we use a mouse model mimicking paediatric antibiotic use and find that therapeutic-dose pulsed antibiotic treatment (PAT) with a beta-lactam or macrolide alters both host and microbiota development. Early-life PAT accelerates total mass and bone growth, and causes progressive changes in gut microbiome diversity, population structure and metagenomic content, with microbiome effects dependent on the number of courses and class of antibiotic. Whereas control microbiota rapidly adapts to a change in diet, PAT slows the ecological progression, with delays lasting several months with previous macrolide exposure. This study identifies key markers of disturbance and recovery, which may help provide therapeutic targets for microbiota restoration following antibiotic treatment.

The potential recovery of the human gut microbiota after an antibiotic treatment, and its effects on our health, are poorly understood. Here, the authors use a mouse model mimicking paediatric antibiotic use to shed new light into these processes.

Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism

Background

Enzymes are known as the molecular machines that drive the metabolism of an organism; hence identification of the full enzyme complement of an organism is essential to build the metabolic blueprint of that species as well as to understand the interplay of multiple species in an ecosystem. Experimental characterization of the enzymatic reactions of all enzymes in a genome is a tedious and expensive task. The problem is more pronounced in the metagenomic samples where even the species are not adequately cultured or characterized. Enzymes encoded by the gut microbiota play an essential role in the host metabolism; thus, warranting the need to accurately identify and annotate the full enzyme complements of species in the genomic and metagenomic projects. To fulfill this need, we develop and apply a method called ECemble, an ensemble approach to identify enzymes and enzyme classes and study the human gut metabolic pathways.

Results

ECemble method uses an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences and also identifies the enzyme classes and subclasses at the finest resolution. A tenfold cross-validation result shows accuracy between 97 and 99% at different levels in the hierarchy of enzyme classification, which is superior to comparable methods. We applied ECemble to predict the entire complements of enzymes from ten sequenced proteomes including the human proteome. We also applied this method to predict enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. After mapping the known and predicted enzymes to canonical human pathways, we identified 48 pathways that have at least one bacteria-encoded enzyme, which demonstrates the complementary role of gut microbiome in human gut metabolism. These pathways are primarily involved in metabolizing dietary nutrients such as carbohydrates, amino acids, lipids, cofactors and vitamins.

Conclusions

The ECemble method is able to hierarchically assign high quality enzyme annotations to genomic and metagenomic data. This study demonstrated the real application of ECemble to understand the indispensable role played by microbe-encoded enzymes in the healthy functioning of human metabolic systems.

Oxalobacter formigenes Colonization and Oxalate Dynamics in a Mouse Model

Animal and human studies have provided compelling evidence that colonization of the intestine with Oxalobacter formigenes reduces urinary oxalate excretion and lowers the risk of forming calcium oxalate kidney stones. The mechanism providing protection appears to be related to the unique ability of O. formigenes to rely on oxalate as a major source of carbon and energy for growth. However, much is not known about the factors that influence colonization and host-bacterium interactions. We have colonized mice with O. formigenes OxCC13 and systematically investigated the impacts of diets with different levels of calcium and oxalate on O. formigenes intestinal densities and urinary and intestinal oxalate levels. Measurement of intestinal oxalate levels in mice colonized or not colonized with O. formigenes demonstrated the highly efficient degradation of soluble oxalate by O. formigenes relative to other microbiota. The ratio of calcium to oxalate in diets was important in determining colonization densities and conditions where urinary oxalate and fecal oxalate excretion were modified, and the results were consistent with those from studies we have performed with colonized and noncolonized humans. The use of low-oxalate purified diets showed that 80% of animals retained O. formigenes colonization after a 1-week dietary oxalate deprivation. Animals not colonized with O. formigenes excreted two times more oxalate in feces than they had ingested. This nondietary source of oxalate may play an important role in the survival of O. formigenes during periods of dietary oxalate deprivation. These studies suggest that the mouse will be a useful model to further characterize interactions between O. formigenes and the host and factors that impact colonization.

Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms.

Screening of different probiotic strains for their in vitro ability to metabolise oxalates: any prospective use in humans?

BACKGROUND

Oxalate is the salt-forming ion of oxalic acid and can generate oxalate salts combining with various cations, such as sodium, potassium, magnesium, and calcium. Approximately 75% of all kidney stones are composed primarily of calcium oxalate (CaOx) and hyperoxaluria, a condition involving high urinary oxalate concentration, is considered a primary risk factor for kidney stone formation, known as nephrolithiasis. Current therapeutic strategies often fail in their compliance or effectiveness, and CaOx stone recurrence is still common. After an initial stone, there is a 50% chance of forming a second stone within 7 years if the condition is left untreated. The potential therapeutic application of some probiotics, mainly lactobacilli and bifidobacteria, in reducing hyperoxaluria in vivo through intestinal oxalate degrading activity is compelling and initial reports are promising. This study was undertaken to screen different Lactobacillus and Bifidobacterium strains for their capacity to degrade oxalate in vitro using reverse-phase high-performance liquid chromatography (HPLC).

METHODS

The oxalate-degrading activity of 13 lactobacilli and 5 bifidobacteria was tested using a novel HPLC method after growth in a broth culture added with 10 mM ammonium oxalate. Experiments were repeated 3 times. Oxalobacter formigenes (DSM 4420) was used as positive reference to validate HPLC oxalate-degrading capability assays.

RESULTS

Lactobacillus strains were more efficient than bifidobacteria in degrading oxalates. L. paracasei LPC09 (DSM 24243) gave the best result, as 68.5% of ammonium oxalate was converted at the end of incubation, whereas the following best converters belong to the L. gasseri and L. acidophilus species. The relatively low conversion rate observed for most bifidobacteria can probably be attributed to intrinsic oxalate toxicity toward this genus.

CONCLUSIONS

Humans lack the enzymes needed to directly metabolise oxalate, and this potentially toxic compound is, therefore, managed using alternative pathways. As oxalate-degrading bacteria are present in the endogenous microbiota of the human intestine, although with significant individual differences, it is possible to hypothesise that the administration of selected oxalate-degrading probiotics could be an alternative and innovative approach to reducing the intestinal absorption of oxalate and the resulting urinary excretion.

The gastrointestinal tract of the white-throated Woodrat (Neotoma albigula) harbors distinct consortia of oxalate-degrading bacteria

The microbiota inhabiting the mammalian gut is a functional organ that provides a number of services for the host. One factor that may regulate the composition and function of gut microbial communities is dietary toxins. Oxalate is a toxic plant secondary compound (PSC) produced in all major taxa of vascular plants and is consumed by a variety of animals. The mammalian herbivore Neotoma albigula is capable of consuming and degrading large quantities of dietary oxalate. We isolated and characterized oxalate-degrading bacteria from the gut contents of wild-caught animals and used high-throughput sequencing to determine the distribution of potential oxalate-degrading taxa along the gastrointestinal tract. Isolates spanned three genera: Lactobacillus, Clostridium, and Enterococcus. Over half of the isolates exhibited significant oxalate degradation in vitro, and all Lactobacillus isolates contained the oxc gene, one of the genes responsible for oxalate degradation. Although diverse potential oxalate-degrading genera were distributed throughout the gastrointestinal tract, they were most concentrated in the foregut, where dietary oxalate first enters the gastrointestinal tract. We hypothesize that unique environmental conditions present in each gut region provide diverse niches that select for particular functional taxa and communities.

Update on the evaluation of repeated stone formers

Office management of stone disease is an important component of a urologist's practice. Evaluation should include analysis of stone composition, 24-hour urine studies, identification of modifiable risk factors, and targeted dietary, lifestyle, and/or medical therapy. A sizeable portion of investigated etiologies and risk factors for stone disease have centered on the complex interplay between obesity, diabetes, and other disease states that comprise the metabolic syndrome. Alternatives to traditional preventive therapy, such as probiotics and various fruit juices, are still being studied but may prove useful adjuncts to traditional preventive therapy, where the mainstays remain increased fluid intake, dietary modification, and pharmacologic therapy. Future studies on preventive therapy of urolithiasis are likely to focus on strategies to increase compliance, cost-effectiveness, and systems-based implementation.

YfdW and YfdU are required for oxalate-induced acid tolerance in Escherichia coli K-12

Escherichia coli has several mechanisms for surviving low-pH stress. We report that oxalic acid, a small-chain organic acid (SCOA), induces a moderate acid tolerance response (ATR) in two ways. Adaptation of E. coli K-12 at pH 5.5 with 50 mM oxalate and inclusion of 25 mM oxalate in pH 3.0 minimal challenge medium separately conferred protection, with 67% ± 7% and 87% ± 17% survival after 2 h, respectively. The combination of oxalate adaptation and oxalate supplementation in the challenge medium resulted in increased survival over adaptation or oxalate in the challenge medium alone. The enzymes YfdW, a formyl coenzyme A (CoA) transferase, and YfdU, an oxalyl-CoA decarboxylase, are required for the adaptation effect but not during challenge. Unlike other SCOAs, this oxalate ATR is not a part of the RpoS regulon but appears to be linked to the signal protein GadE. We theorize that this oxalate ATR could enhance the pathogenesis of virulent E. coli consumed with oxalate-containing foods like spinach.

Impact of oxalic acid on rumen function and bacterial community in sheep

Oxalic acid (OA) is a secondary compound occurring in a wide range of plants consumed by ruminants, especially in saline lands or in arid and semi-arid regions. However, its impact on the rumen microbial community and its changes over time, as well as the potential consequences on ruminal function, remain unknown. To examine this impact, five ewes fitted with a ruminal cannula and fed low-quality grass hay were dosed daily with 0.6 mmol of OA/kg body weight through the cannula for 14 days. On days 0 (before the start), 4, 7 and 14 of the administration period, samples of ruminal digesta were collected throughout the day (0, 3, 6 and 9 h after the morning feeding) for analysis of the bacterial community and fermentation parameters (pH, ammonia and volatile fatty acid (VFA) concentrations). In addition, two feedstuffs were incubated in situ using the nylon bag technique to estimate ruminal degradation. Terminal restriction fragment length polymorphism was employed to monitor the dynamics of total bacteria, and quantitative real-time PCR was used to investigate the abundance of the oxalate-degrading Oxalobacter formigenes. Neither pH nor total VFA concentrations were affected. Nevertheless, OA dosing altered molar proportions of most individual VFA and ammonia concentrations (P < 0.001). The dry matter disappearance of alfalfa hay was reduced on days 7 and 14 and that of barley straw only on day 7 (P < 0.01). These slight changes were related to others observed in the relative frequency of a number of terminal restriction fragments. Variations in the ruminal microbiota occurred rapidly with OA administration, which did not modify the bacterial diversity significantly but altered the structure of the community. However, many of these changes were reversed by the end of the experiment, with no significant differences between days 0 and 14 of dosing. These results suggest a rapid adaptation of the rumen bacterial community linked to the estimated increase in the abundance of O. formigenes (from 0.002% to 0.007% of oxc gene in relation to the total bacteria 16S rDNA; P < 0.01), which is assumed to be responsible for oxalate breakdown.

Comparative faecal microbiota of dogs with and without calcium oxalate stones

AIMS

The absence of enteric oxalate-metabolizing bacterial species (OMBS) increases the likelihood of calcium oxalate (CaOx) urolithiasis in humans and dogs. The goal of this study was to compare the gut microbiota of healthy dogs and CaOx stone formed dogs (CaOx-dogs), especially with respect to OMBS.

METHODS AND RESULTS

Faecal samples from healthy and CaOx-dogs were obtained to analyse the hindgut microbiota by sequencing the V3 region of bacterial 16S rDNA. In total, 1223 operational taxonomic units (OTUs) were identified at 97% identity. Only 38% of these OTUs were shared by both groups. Significant differences in the relative abundance of 152 OTUs and 36 genera were observed between the two groups of dogs.

CONCLUSIONS

The faecal microbiota of healthy dogs is distinct from that of CaOx-dogs, indicating that the microbiota is altered in CaOx-dogs.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study that has compared the gut microbial diversity in healthy and CaOx-dogs. Results of this study indicate the future need for functional and comparative analyses of the total array of oxalate-metabolizing genes between healthy and CaOx stone formers, rather than focusing on specific bacterial species, to understand the critical role of OMBS in CaOx urolithiasis.

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.

Defining microbiota for developing new probiotics

The human body harbors complex communities of microbes that play a prominent role in human health. Detailed characterization of the microbiota in the target population forms the basis of probiotic use. Probiotics are defined as live bacterial preparations with clinically documented health effects in humans, and independent of their genus and species, probiotic strains are unique and their beneficial properties on human health have to be assessed in a case-by-case manner. Understanding the mechanisms by which probiotics influence microbiota would facilitate the use of probiotics for both dietary management and reduction in risk of specific diseases. The development of high throughput sequencing methods has allowed metagenomic approaches to study the human microbiome. These efforts are starting to generate an inventory of bacterial taxons and functional features bound to particular health or disease status that allow inferring aspects of the microbiome's function. In the future, this information will allow the rational design of dietary interventions aimed to improve consumer's health via modulation of the microbiota.

[Probiotics and pregnancy]

Prenatal care is one of the great challenges in medicine. Aims of therapies and protocols may influence the life of mothers and babies. Diseases occurring during pregnancy are even more dangerous, because of the difficulties in their treatment strategy. Prevention must be emphasized using safe and natural drugs. Pre- and probiotics are in focus of the medical sciences. Various publications and studies emphasize the importance of these drugs in evidence-based medicine. Safe methods are essential in prenatal care. Authors review published data on the effect and potential use of pre- and probiotics during pregnancy.