Navigating the relentless cycle of recurrent urinary tract infections (UTIs) can be a source of significant frustration and discomfort for many. This persistent health challenge often leaves individuals seeking answers beyond conventional treatments, yearning for a lasting solution to their recurrent plight.

The aim of this blog is to delve into the critical role ammonia plays in the persistence of urinary tract infections (UTIs) and to shed light on how employing targeted diagnostic tests can transform the management and treatment of chronic UTIs, paving the way for more effective and personalized strategies

The Science Behind Ammonia and UTIs

Ammonia is a compound with the formula NH3, produced in the body primarily as a waste product of protein metabolism. Normally, it’s converted into urea in the liver through the urea cycle and then excreted by the kidneys in urine. This conversion is crucial as ammonia is toxic at high levels, especially to the brain. Proper management and excretion are essential for maintaining the body’s pH balance and overall health.

Hyperammonemia occurs when the blood ammonia level rises above normal, potentially leading to neurological and other systemic health issues. The most common cause of hyperammonemia is liver dysfunction, which can result from conditions like cirrhosis or acute liver failure. This condition can severely affect the brain, leading to symptoms ranging from mild cognitive impairment to severe encephalopathy. The brain is particularly vulnerable to the effects of hyperammonemia, especially during developmental stages. Ammonia is toxic to the brain because it can lead to astrocyte swelling, impair neurotransmission, and contribute to the generation of oxidative stress. These effects are mediated through mechanisms such as increased glutamine synthesis, which exceeds the brain’s capacity to process ammonia, leading to elevated ammonia levels and consequent brain damage​ (Limón, Angulo-Cruz et al. 2021).

Elevated ammonia levels in the body can have a direct impact on urinary tract health, contributing to chronic urinary tract infections (UTIs) and other health issues. Normally, the urinary system effectively clears waste products, including ammonia, from the body. However, when ammonia levels are high, it can alter the pH balance of urine, making the urinary tract more susceptible to infections. High ammonia can encourage the growth of bacteria by providing an environment where pathogens can thrive, leading to recurrent UTIs.

Moreover, elevated ammonia levels can damage the mucosal lining of the urinary tract, weakening its natural defenses against infections. This damage not only facilitates the adherence and colonization of bacteria but also impairs the body’s ability to clear these infections effectively. Additionally, high ammonia can lead to systemic effects, such as impairing immune function, further compromising the body’s ability to fight off urinary and other infections. Understanding the link between ammonia levels and UTI risk is crucial for developing targeted strategies to manage and prevent these chronic conditions effectively.

Symptoms of excessive ammonia

Beyond its impact on urinary tract health, hyperammonemia, or elevated ammonia levels in the blood, can lead to a range of symptoms affecting various parts of the body, providing a clearer picture of its systemic effects. These symptoms include:

  • Neurological Changes: Confusion, lethargy, and changes in behavior can occur due to ammonia’s toxic effects on the brain. In severe cases, it can lead to encephalopathy, a decline in brain function.
  • Gastrointestinal Issues: Ammonia can disrupt gut health, leading to symptoms such as nausea, vomiting, and abdominal pain.
  • Muscular Symptoms: Weakness and muscle cramps are common as ammonia interferes with normal muscle function.
  • Mood Alterations: Irritability and mood swings can result from the impact of ammonia on the central nervous system.
  • Fatigue: Persistent tiredness may occur, not necessarily linked to exertion or lack of sleep, as the body’s energy production pathways are affected.

Recognizing these symptoms can be crucial for individuals dealing with persistent health issues, including chronic UTIs, as they may point towards underlying issues with ammonia metabolism that need to be addressed for overall health improvement.

Diagnostic Tools: Beyond the Basics

In the quest to uncover the root causes of chronic urinary tract infections (UTIs) and associated conditions, advanced diagnostic tools offer a window into the body’s intricate biochemical landscape. Among these, the organic acid test, amino acid analysis, and hair tissue mineral analysis stand out for their ability to provide comprehensive insights into an individual’s metabolic processes, nutrient status, and potential exposure to toxins.

  • Organic Acid Test (OAT): This powerful urine test evaluates over 70 markers of metabolism, including those related to the gut microbiome, nutrient deficiencies, and the body’s cellular energy production. By identifying abnormalities in metabolic pathways, OAT can suggest specific nutritional interventions to correct these imbalances.
  • Amino Acid Analysis: Performed on a blood or urine sample, this test measures levels of amino acids, the building blocks of proteins. Imbalances in amino acids can indicate problems with digestion, absorption, metabolic pathways, and nutrient deficiencies, impacting everything from mood to muscle function.
  • Hair Tissue Mineral Analysis (HTMA): By analyzing mineral content in hair, HTMA provides insights into long-term exposure to toxic metals and the status of essential minerals within the body. This test helps to uncover mineral imbalances and heavy metal toxicity that can contribute to a range of health issues, including chronic UTIs.
  • Polymerase Chain Reaction (PCR) and next-generation sequencing (NGS) are powerful tools for identifying bacterial overgrowth in the urine, playing a pivotal role in diagnosing and managing chronic urinary tract infections (UTIs). These advanced molecular techniques offer a level of sensitivity and specificity far beyond traditional urine cultures, allowing for the detection of a broad spectrum of pathogenic and commensal bacteria that may contribute to recurrent UTIs.
  • PCR works by amplifying specific DNA sequences of bacteria present in urine samples, making it possible to identify pathogens even when present in very low quantities. This technique is especially useful for detecting bacteria that are difficult to grow in culture or are present at levels below the detection threshold of standard microbiological methods.
  • Next-generation sequencing, on the other hand, goes a step further by sequencing the DNA of all microorganisms in a sample, providing a comprehensive overview of the urinary microbiome. NGS can identify a wide range of pathogens, including bacteria, fungi, and viruses, and offer insights into the bacterial diversity and abundance in the urinary tract. This detailed information is crucial for understanding the complex interplay between different microbial species and their role in UTI pathogenesis.
  • By identifying the specific pathogens involved in chronic UTIs, PCR and NGS enable healthcare providers to tailor antibiotic therapy to the individual’s infection, potentially increasing treatment efficacy and reducing the risk of antibiotic resistance. Moreover, these methods can uncover bacterial strains that traditional cultures may miss, offering a more accurate diagnosis for patients with persistent symptoms but negative culture results.
  • In conclusion, PCR and next-generation sequencing represent significant advancements in the diagnostic arsenal against chronic UTIs, offering a deeper understanding of urinary tract microbiology and facilitating personalized treatment approaches.

Together, these diagnostic tools offer a holistic view of a patient’s health, allowing for targeted treatment strategies that address the underlying causes of chronic conditions, rather than just managing symptoms.

Let’s dive deeper into these tests

These advanced diagnostic tests delve deep into the body’s biochemical processes to identify markers that are crucial in understanding ammonia’s role in chronic urinary tract infections (UTIs) and related health issues:

  • Orotate, Arginine, Citrulline, Ornithine, and Alpha-Ketoglutarate (Organic Acid Test & Amino Acid Analysis): These markers are integral to the urea cycle, the body’s primary pathway for ammonia detoxification. Abnormal levels can indicate disruptions in the urea cycle, leading to elevated ammonia. Elevated ammonia levels can compromise the urinary tract’s defense mechanisms, making it more susceptible to infections.
  • Measuring orotic acid in the urine is a diagnostic method used to detect disorders related to ammonia metabolism, particularly urea cycle disorders (UCDs). Orotic aciduria, or elevated levels of orotic acid in urine, can indicate an excess of ammonia in the body. Since the urea cycle is responsible for converting ammonia into urea for excretion, any disruptions in this cycle can lead to ammonia accumulation, which is then indirectly identified through increased orotic acid in urine tests.
  • Ornithine and arginine are integral to the urea cycle, the body’s primary method of ammonia detoxification. Ornithine acts as a carrier, facilitating the removal of ammonia by converting it into urea, while arginine is a byproduct of this process but also serves as a precursor for creating more ornithine. If either amino acid is deficient, the cycle can’t efficiently process ammonia, leading to its accumulation in the body. This imbalance can hint at underlying metabolic issues, often associated with urea cycle disorders.
  • Citrate and Aconitase (Organic Acid Test): Citrate levels can reveal insights into the Krebs cycle (a key energy-producing process), where aconitase plays a critical role. Imbalances here may affect cellular energy and the body’s ability to combat infections, including UTIs.
    • Elevations of citrate in the context of elevated ammonia could be indicative of disruptions in the citric acid cycle (TCA or Krebs cycle), which is closely linked to the urea cycle. Citrate accumulates when the TCA cycle is inhibited or slowed, which can happen due to the diversion of aspartate and other intermediates to ammonia detoxification in the urea cycle. This can reflect a metabolic adaptation to handle increased ammonia, suggesting an underlying issue with ammonia processing or a related metabolic dysfunction.
  • Elevated citrulline levels could indicate a block in the argininosuccinate synthetase (ASS) enzyme, essential for converting citrulline to arginine in the urea cycle, leading to ammonia accumulation.
  • Infections, like UTIs caused by certain bacteria, can reduce arginine levels and increase citrulline and ammonia. Magnesium and aspartic acid are crucial for this metabolic pathway, and Vitamin B1 (thiamine) supplementation can help lower ammonia levels by improving the metabolic flux through this pathway.
  • When citrulline levels are high, it might signal a block in the ASS enzyme, crucial for converting citrulline to arginine in the urea cycle. This block can lead to ammonia buildup. Certain bacteria in UTIs consume arginine, produce citrulline, and elevate ammonia levels. The reaction converting citrulline to arginine needs magnesium and aspartic acid. Vitamin B1 (thiamine) supplementation can help reduce ammonia by enhancing the efficiency of this metabolic process.
  • Manganese and Iron (Hair Tissue Mineral Analysis): Manganese and iron are crucial for numerous enzymatic reactions in the body, including those involved in fighting infections. Imbalances in these minerals can indicate oxidative stress and inflammation, potentially exacerbating the risk of chronic UTIs.

By pinpointing deviations in these markers, healthcare providers can tailor interventions to restore balance to the body’s metabolic processes. This targeted approach not only addresses the immediate concern of recurrent UTIs but also contributes to the overall well-being and health of the urinary tract and the body as a whole.

Interpreting Test Results: A Gateway to Personalized Treatment

Interpreting the results from organic acid tests, amino acid analysis, and hair tissue mineral analysis offers healthcare professionals a detailed map of underlying biochemical imbalances that may contribute to chronic urinary tract infections (UTIs). By identifying specific markers related to ammonia production and metabolism, such as orotate, arginine, citrulline, ornithine, alpha-ketoglutarate, citrate, aconitase, as well as mineral levels like manganese and iron, practitioners can pinpoint disruptions in the body’s natural processes that may predispose individuals to recurrent UTIs.

Targeted treatment strategies can then be developed to address these root causes. For example, if test results indicate a disruption in the urea cycle leading to elevated ammonia levels, interventions may include dietary modifications to reduce ammonia production, supplements to support the urea cycle, or probiotics to balance the gut microbiota, where a significant portion of ammonia production occurs. If mineral imbalances are identified, supplementation or dietary adjustments can help restore optimal levels, potentially reducing inflammation and bolstering the body’s defense against pathogens.

This approach goes beyond treating the symptoms of UTIs with antibiotics, which can lead to resistance and do not address the underlying imbalances that contribute to the chronic nature of these infections. By understanding and correcting these foundational issues, healthcare providers can offer patients a long-term solution to recurrent UTIs, improving overall health and quality of life.


Imagine a patient, whom we’ll call Alex, who struggled with persistent bladder issues and recurrent urinary tract infections (UTIs). Traditional treatments had offered only temporary relief, and Alex was searching for a more lasting solution.

Advanced diagnostic tests, including an organic acid test, amino acid analysis, and hair tissue mineral analysis, and Microgen testing revealed a complex picture. The tests identified urinary pathogens indicative of excessive ammonia production and several critical markers of hyperammonemia: high orotate levels, low ornithine, elevated alpha-ketoglutarate, increased citrate, and magnesium deficiency.

These results provided valuable insights into the underlying issues contributing to Alex’s chronic UTIs. The high level of orotate and imbalance in the amino acids suggested a disruption in the urea cycle, leading to ammonia accumulation. This imbalance not only exacerbated Alex’s bladder issues but also affected overall health.

To address these underlying issues, a targeted intervention was designed. The treatment plan included:

  • Magnesium supplementation to address the deficiency and support overall metabolic health.
  • Ornithine supplementation to aid in the urea cycle, helping to reduce ammonia levels.
  • Nutritional support for the citric acid cycle, including Vitamin B3 (Niacin), additional magnesium, and manganese, to improve energy production and reduce ammonia accumulation.
  • Modification of Alex’s protein intake to reduce the load on the urea cycle, preventing excessive ammonia production.

Over the course of treatment, Alex experienced a significant improvement in symptoms. Not only did the recurrent UTIs become less frequent, but Alex also noted an overall increase in energy and well-being.

This case study highlights the importance of comprehensive diagnostic testing in identifying the root causes of chronic health issues. By understanding the specific imbalances and deficiencies in the body, healthcare providers can tailor interventions to address these issues directly, leading to more effective and lasting treatments.

Manganese- a lesson learned when studying hepatic encephalopathy (HE)

Manganese, on the other hand, is an essential trace element but can become neurotoxic at elevated levels. The relationship between manganese and hyperammonemia becomes particularly relevant in the context of hepatic encephalopathy (HE), a complex condition arising from liver disease which can lead to neuropsychiatric abnormalities. In chronic liver disease, one of the findings is the bilateral, symmetric T1 hyperintensity in the brain regions such as the globus pallidi, which is commonly attributed to manganese accumulation. This accumulation is believed to result from portosystemic shunting that bypasses liver uptake of manganese, which is critical since the liver plays a vital role in regulating manganese levels in the body. The accumulation of manganese in the brain is a factor in the development of hepatic encephalopathy, underscoring the intricate link between liver function, ammonia, and manganese levels in the body​ (EMCrit Project)​.

Diagnosing Hepatic Encephalopathy (HE) is a complex process because there is no single test that definitively identifies the condition. The diagnosis typically involves a combination of evaluating your medical history, observing your symptoms, and conducting a thorough clinical exam. Blood tests may be performed to check for liver and kidney dysfunction, infections, and other conditions that could contribute to HE. These tests, however, are not specific to HE and are used more to aid in making the diagnosis based on history and symptoms. Imaging tests, such as MRI and CT scans, might be ordered to rule out other types of brain disease or damage, and an EEG might be used to look for brain wave changes associated with HE. Essentially, HE is often diagnosed through exclusion, meaning other potential causes for the symptoms are ruled out​ (American Liver Foundation)​.

The grading of hepatic encephalopathy symptoms, according to the Cleveland Clinic, is based on their severity, ranging from Grade 0 (minimal changes) to Grade 4 (coma). This system helps in assessing the condition’s impact on cognitive and motor functions, which is crucial for treatment planning. The causes of HE are primarily related to liver dysfunction that leads to an inability to filter neurotoxins from the blood, which can result from acute liver failure, chronic liver failure, or a portosystemic shunt. Diagnosis is typically made by a hepatologist or gastroenterologist through symptom evaluation, assessing the underlying liver condition, and ruling out other causes. Tests used in the diagnostic process can include blood tests for liver function and ammonia levels, Doppler ultrasound for liver blood flow assessment, brain imaging tests, and EEG for brain activity​ (Cleveland Clinic)​.

Understanding the diagnosis process and the types of hepatic encephalopathy is critical for managing the condition effectively and preventing its progression. Early detection and treatment are key to managing HE and can significantly affect the prognosis and quality of life for those affected by this condition.

Note- individuals without hepatic encephalopathy (HE) can still experience dysregulation in ammonia metabolism due to liver impairments, urea cycle disorders (UCDs), or potentially magnesium deficiency, affecting manganese metabolism. Hyperammonemia, an excess of ammonia in the blood, can occur due to liver disease, decreased blood flow to the liver, or urea cycle disorders, leading to impaired conversion of ammonia into urea. UCDs are congenital conditions affecting the enzymes necessary for the urea cycle, causing acute or chronic hyperammonemia, which can be triggered by illness or stress at any life stage​ (Cleveland Clinic)

Lifestyle, Diet, and Ammonia: Finding Balance

Diet, magnesium levels, and the efficiency of the urea cycle play pivotal roles in managing ammonia levels in the body, influencing urinary tract health and the risk of UTIs. Here’s how these factors interconnect and practical steps to mitigate their impact:

High Protein Diets

High protein diets can increase ammonia production because protein metabolism generates ammonia as a byproduct. While the body typically converts ammonia into urea for excretion, excessive protein intake can overburden this process, leading to higher ammonia levels. To manage this:

  • Moderate Protein Intake: Aim for a balanced diet that meets protein needs without excess. Consider plant-based proteins, which may produce less ammonia.
  • Stay Hydrated: Ample water intake helps facilitate urea excretion, minimizing ammonia accumulation.

Magnesium Deficiency

Magnesium plays a critical role in numerous enzymatic reactions, including those in the urea cycle. A deficiency can disrupt this cycle, impairing the body’s ability to convert ammonia into urea. To address magnesium deficiency:

  • Magnesium-Rich Foods: Incorporate foods high in magnesium, such as leafy greens, nuts, seeds, and whole grains, into your diet.
  • Supplementation: Consider magnesium supplements, especially if dietary adjustments are insufficient. Consult a healthcare provider for appropriate dosage.

Urea Cycle Defects

Inherited urea cycle defects can severely affect the body’s ability to process ammonia. While these conditions often require medical intervention, certain lifestyle adjustments can help manage ammonia levels:

  • Dietary Management: Work with a healthcare provider or dietitian to adjust protein intake suitably. They may recommend a specific diet that limits certain amino acids.
  • Ammonia Scavengers: In some cases, medications that help remove ammonia from the bloodstream may be prescribed.

Lifestyle Changes to Reduce UTI Risk

  • Cranberry Consumption: Regular consumption of cranberry juice or supplements may help prevent UTIs by inhibiting bacteria from adhering to the bladder wall.
  • Probiotics: Incorporating probiotic-rich foods or supplements can support a healthy urinary tract by promoting beneficial bacteria growth.
  • Avoiding Irritants: Minimize bladder irritants like caffeine, alcohol, and spicy foods, which can exacerbate UTI symptoms.

By understanding the intricate relationship between diet, magnesium deficiency, urea cycle efficiency, and ammonia levels, individuals can make informed choices to manage their health proactively. Reducing ammonia levels through dietary adjustments and lifestyle changes not only supports overall well-being but also diminishes the risk of chronic UTIs, fostering a healthier urinary tract environment.

In wrapping up, it’s vital to recognize the significant role that ammonia plays in the development and persistence of chronic urinary tract infections (UTIs). By delving into the intricacies of how elevated ammonia levels can compromise urinary tract health, we uncover a more profound understanding of these infections. The use of comprehensive diagnostic tools, such as the organic acid test, amino acid analysis, and hair tissue mineral analysis, offers a beacon of hope. These tests enable us to pinpoint specific biochemical imbalances, guiding us toward targeted treatment strategies that address the root cause rather than merely treating symptoms.

Looking ahead, there’s a promising horizon for individuals battling chronic UTIs. The shift towards a nuanced approach—considering each person’s unique biochemical landscape—heralds a new era in personalized healthcare. This approach not only promises more effective management of chronic UTIs but also enhances overall well-being by addressing underlying imbalances. As we continue to explore and understand the complex interplay between ammonia levels and urinary tract health, our optimism grows for a future where chronic UTIs are no longer a daunting challenge but a manageable condition with tailored, effective solutions.



American Liver Foundation . (n.d.). Diagnosing hepatic encephalopathy. Diagnosing Hepatic Encephalopathy (HE) FacebookTwitterEmailPrintShare. https://liverfoundation.org/liver-diseases/complications-of-liver-disease/hepatic-encephalopathy/diagnosing-hepatic-encephalopathy/

Cleveland Clinic . (n.d.). Hyperammonemia. https://my.clevelandclinic.org/. https://my.clevelandclinic.org/health/diseases/24065-hyperammonemia

Limón, I. D., et al. (2021). “Disturbance of the Glutamate-Glutamine Cycle, Secondary to Hepatic Damage, Compromises Memory Function.” Front Neurosci 15.