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Could Food Poisoning Be The Reason For Your Chronic Digestive Symptoms?

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Could Food Poisoning Be The Reason For Your Chronic Digestive Symptoms?

If you've experienced chronic digestive symptoms ever since an acute bout of food poisoning, you're not alone. Based on pooled data from 29 studies, up to 85.5% of people develop post-infection irritable bowel syndrome (PI-IBS) after acute gastroenteritis (AGE). In this article, we'll discuss what these terms mean, the pathophysiology involved in transitioning from acute food poisoning to chronic digestive problems, and what you can do about it.  


What is Acute Food Poisoning?

Acute food poisoning, otherwise known as foodborne gastroenteritis, is inflammation of the lining of the stomach and intestines after exposure to a contaminated food or beverage with a germ or other harmful substance, including bacteria, viruses, parasites, chemicals, or mycotoxins. In the United States, 48 million people contract a foodborne illness, and 3,000 die of one annually (24).  

The table below lists common microbes that are responsible for causing food poisoning:

Microbes threaten food safety at various stages, including growth, harvesting, processing, storage, shipping, and preparation. Foods susceptible to microbial contamination include fresh produce, raw or undercooked animal products, unpasteurized dairy products, deli foods, and improperly canned or sealed items. The presence of harmful microbes in these foods can occur at any point in the supply chain, emphasizing the importance of proper handling and preparation to ensure food safety. (45

The onset of symptoms is usually rapid, occurring within hours to a few days after consuming contaminated food. Symptom duration can also vary, lasting from a few hours to several days. Symptoms are usually self-limiting, and individuals recover without specific medical treatment. However, severe cases, especially in vulnerable populations such as the elderly, young children, and immunocompromised individuals, may require medical attention and, in some instances, hospitalization. Common symptoms of gastroenteritis include:

  • Abdominal pain and cramping
  • Nausea and vomiting
  • Diarrhea
  • Fever
  • Loss of appetite
  • Fatigue

Symptoms of severe gastroenteritis that warrant medical attention include: 

  • Bloody diarrhea
  • Diarrhea lasting longer than three days
  • Fever over 102°F
  • Vomiting so often that you cannot keep liquids down
  • Signs of dehydration: infrequent urination, dry mouth and throat, dizziness

The Transition from Acute to Chronic: The Gut Connection

PI-IBS is a condition that can develop after AGE. The pathogenesis of PI-IBS involves a complex interplay of factors. Following the resolution of the initial infection, some individuals experience persistent gastrointestinal symptoms. Evidence reveals that the frequency of PI-IBS is highest after parasitic infections and lowest after viral infections. Other factors that increase the risk of an individual developing PI-IBS include prolonged duration of initial illness, toxicity of infecting agent, smoking, elevated markers of mucosal inflammation, female gender, depression, hypochondriasis, adverse life events preceding the initial illness, and antibiotic treatment for AGE. (22, 38

Multiple mechanisms have been proposed in the pathogenesis of PI-IBS. Collectively, these mechanisms trigger chronic inflammation, disrupt intestinal barrier function, and alter neuromuscular function within the gastrointestinal tract. (46

Exposure to intestinal infection activates chronic, low-grade systemic and mucosal inflammation. Multiple studies have observed increased expression and activation of pro-inflammatory immune markers in patients with IBS. This chronic inflammation induces intestinal hyperpermeability ("leaky gut"). (22, 38

The gut microbiome, which becomes altered during AGE, appears to stay in a residual dysbiotic state after the resolution of the initial infection. Compared to controls, patients with PI-IBS have a greater abundance of Bacteroidetes bacteria and relative reductions in bacteria belonging to the Firmicutes phylum. Dysbiosis perpetuates gastrointestinal inflammation, immune activation, and intestinal permeability. (22, 38

Two specific antibodies have also been implicated in PI-IBS. Cytolethal distending toxin B (CdtB) is a toxin produced by bacteria that cause AGE, including Campylobacter, Salmonella, E. coli, and Shigella dysenteriae. During the acute infection, the immune system creates anti-CdtB antibodies. CdtB resembles vinculin, a protein required for healthy gut function. Because of the similar structures between CdtB and vinculin, the immune system is essentially tricked into producing anti-vinculin antibodies through molecular mimicry. Anti-vinculin antibodies attack interstitial cells of Cajal (ICC) in the gastrointestinal tract, which are responsible for gastrointestinal motility. In this way, AGE induces intestinal dysmotility, one of the contributing factors to functional gastrointestinal disorders (i.e., IBS), and exacerbates the chronic effects of acute gastrointestinal infection.

Common Chronic Symptoms Post-Food Poisoning

After experiencing a bout of food poisoning, individuals may continue to endure persistent digestive issues. Common chronic symptoms after food poisoning include those of irritable bowel syndrome: abdominal pain, altered bowel habits, bloating, abdominal distention, and gas. Most patients with PI-IBS present with either the diarrhea-predominant (IBS-D) or mixed subtype (IBS-M) of IBS (22). A systematic review and meta-analysis demonstrated that the risk of developing IBS symptoms increases six-fold after AGE and remains elevated for at least 2-3 years after the initial infection. The increased risk for and the chronicity of these symptoms can be attributed to the mechanisms described above.

Functional dyspepsia is also common in patients with PI-IBS (22). Symptoms of dyspepsia include:

  • Frequent and bothersome sensation of fullness after eating
  • Early satiety 
  • Stomach pain or burning unrelated to bowel movements

Diagnosing Post-Infectious Conditions

Diagnosing post-infectious IBS involves a comprehensive evaluation by healthcare professionals to identify and understand the persistent symptoms following an acute gastrointestinal infection. A detailed medical history is typically obtained, including information about the initial infection, the onset and nature of current symptoms, and any relevant personal or family medical history. Clinical assessments may include physical examinations and laboratory tests to rule out other potential causes of gastrointestinal symptoms.

Challenges in post-food poisoning diagnosis arise due to the diverse nature of symptoms and the lack of specific biomarkers. PI-IBS often presents with symptoms that overlap with other gastrointestinal disorders, making it difficult to establish a definitive diagnosis. As a functional gastrointestinal disorder, PI-IBS lacks observable changes to gastrointestinal anatomy; this means that most standard laboratory tests come back as normal despite the presence of symptoms.

A nuanced and patient-centered strategy is crucial to tackling the challenges associated with diagnosing these conditions, which is why functional medicine shines in addressing functional gastrointestinal disorders. Functional medicine providers employ diagnostic tools that distinguish between normal and optimal states. This approach also recognizes the significant impact of external environmental factors, such as stress, on digestive health. By assessing non-standard and functional markers of gastrointestinal health and conducting a thorough patient history that highlights factors like diet, hydration, sleep, and stress management, these providers are better equipped to identify imbalances contributing to digestive symptoms compared to their conventional counterparts.

Functional Medicine Lab Testing

An initial and routine medical evaluation for patients presenting with IBS symptoms includes CBC, CMP, CRP, fecal calprotectin, and stool culture/microscopy to rule out infectious pathogens. With severe symptoms, testing and imaging to rule out celiac disease, microscopic colitis, and inflammatory bowel disease (IBD) are also warranted. (22)

However, as mentioned above, these tests generally come back normal in patients with PI-IBS, indicating the need for additional testing that is not routinely ordered in the conventional medical setting. Functional medicine providers commonly order the following tests during the diagnostic evaluation of chronic digestive symptoms:  


Measuring anti-CdtB and anti-vinculin antibodies helps diagnose PI-IBS. The ibs-smart test by Gemelli Biotech is one panel that measures both antibodies with a single blood sample.

SIBO Breath Test

At least one-fifth of patients with IBS-D have small intestinal bacterial overgrowth (SIBO), a condition characterized by bacterial overgrowth in the small intestine. As research has expanded our knowledge on this condition, we now understand that there are three distinct subtypes of SIBO: hydrogen-dominant SIBO, hydrogen sulfide-dominant SIBO, and intestinal methanogen overgrowth (IMO). A glucose or lactulose hydrogen breath test, both from Commonwealth Diagnostics International, can be performed by patients at home to diagnose SIBO or IMO in patients with PI-IBS. 

Comprehensive Stool Analysis

A comprehensive stool analysis provides a complete view into gut health to assess patient recovery from AGE and identify lingering imbalances in the gut microbiome, immune function, and digestion that often contribute to chronic digestive symptoms. These comprehensive stool tests go beyond the standard screening for infectious pathogens to measure the diversity and abundance of the beneficial gut microbes, along with screening for overgrowth of pathogenic and opportunistic bacteria, viruses, parasites, and yeast that are less commonly measured on standard stool panels. 


An estimated one-tenth of patients with PI-IBS have malabsorption syndrome, which is when the small intestine does not digest and absorb carbohydrates, fats, proteins, and/or micronutrients. Along with the comprehensive stool analysis, which screens for protein and fat malabsorption, breath tests can diagnose fructose, lactose, or sucrose intolerance/malabsorption.

Food Intolerances 

Adverse food reactions are strong contributors to IBS symptoms, with up to 65% of patients with IBS reporting specific food-related symptoms. Patients with IBS commonly report removing wheat, dairy, eggs, coffee, yeast, potatoes, and citrus from their diets is helpful (38).


Treatment and Management Strategies

Treating chronic digestive symptoms following food poisoning encompasses a multifaceted approach, addressing both the symptoms and underlying factors contributing to the persistence of gastrointestinal issues. Functional medicine providers customize treatment plans based on individualized patient history and lab results. The 5R gut healing protocol is a holistic approach designed to address various aspects of gut health and promote healing. The five phases, often referred to as the 5Rs, are as follows:


The first phase involves identifying and eliminating factors contributing to gut dysfunction and inflammation. This includes removing potential irritants such as allergenic or inflammatory foods, pathogens, environmental toxins, emotional stressors, and medications. The goal is to create an environment that minimizes stress on the digestive system. (2, 15) 

Based on food testing results, a doctor may recommend an elimination diet for a minimum of four weeks.

Pharmaceutical medications or natural/herbal antimicrobial agents are often recommended to eradicate pathogenic overgrowth. 


In the replacement phase, the focus is on replenishing digestive enzymes that may be deficient. This could involve supplementation with hydrochloric acid, pancreatic enzymes, or bile acids to support proper digestion and nutrient absorption. By enhancing the digestive process, the body is better equipped to extract essential nutrients from food. This phase also emphasizes using diet and supplements to replace deficient nutrients identified with testing. (2, 15)


This phase aims to restore a healthy balance of gut microbiota by introducing beneficial bacteria, also known as probiotics. Probiotics help promote a diverse and resilient microbial community in the gut, supporting various aspects of digestive and overall health. This may involve taking probiotic and/or prebiotic supplements and consuming fermented foods. (2, 15, 33


The repair phase focuses on healing the gut lining, which may have been compromised by inflammation or damage. This phase aims to reduce intestinal permeability and create an environment conducive to healing. Supplements that support gut mucosal integrity, such as glutamine, zinc, and DGL, may be included in the protocol. (2, 15) 


The final phase, often called the rebalance or maintenance phase, involves adopting long-term strategies to sustain gut health. This includes continuing to support a diverse gut microbiota through healthy lifestyle practices, such as maintaining a balanced and nutritious diet, staying hydrated, managing stress, and exercising regularly. Regular monitoring and adjustments to the protocol may be necessary to address changing needs and ensure ongoing gut health. (2, 15) 

The Role of Diet in Recovery

Dietary management post-food poisoning plays an important role in the recovery and maintenance of optimal gut health. The evidence overwhelmingly shows us that what we eat matters. Plant-based and anti-inflammatory diets promote a healthy microbiome, suppress pathogen growth, and enhance intestinal barrier function. Conversely, excessive red meat, simple carbohydrates, saturated/trans fats, and alcohol have the opposite effect, contributing to a leaky gut, unfavorable shifts in the microbiome, and systemic inflammation. (12

Specific diets tailored to individual needs can significantly contribute to symptom relief and promote the restoration of digestive function. The identification and elimination of trigger foods are central to this process, as certain foods may exacerbate symptoms and hinder recovery. Elimination diets, such as the low-FODMAP diet, can effectively reduce the intake of fermentable carbohydrates that may contribute to bloating, gas, and abdominal discomfort. Spicy foods, dairy, caffeine, alcohol, and artificial sweeteners are common IBS food triggers; avoidance of these can help minimize digestive symptoms. Diets should always be customized based on cultural beliefs and food tolerance levels.

Nutritional support for gut health must also ensure an adequate intake of essential nutrients that play a role in mucosal integrity and gut microbiome health. Probiotic- and prebiotic-rich foods, including yogurt, sauerkraut, kimchi, legumes, garlic, and whole grains, contribute to the restoration of a healthy gut microbiota. Note that these foods may exacerbate digestive symptoms until bacterial overgrowth has been addressed. (10

Nutrients such as glutamine, zinc, omega-3 fatty acids, and vitamins A and D are known for their roles in supporting gut lining repair and reducing inflammation. The table below lists foods rich in each of these gut-healing nutrients: 

(Source: 23,43,18,42,44)

Preventing Recurrence and Promoting Gut Health

As discussed above, the final step in the 5R protocol calls for sustained gut health by adopting healthy lifestyle practices. Chronic stress, sleep disturbances, dehydration, and physical inactivity negatively impact gut health through various mechanisms. Conversely, research suggests that regular stress management practices, adequate sleep, and exercise promote digestive function and a healthy gut microbiome and reduce symptoms of IBS. 

One of the best ways to prevent the recurrence of PI-IBS is to prevent foodborne illness, which involves practicing good hygiene, safe food handling, and making informed choices about food. According to the FDA, these tips help reduce the risk of foodborne illness:

  • Wash hands thoroughly with soap and water before handling food, after using the bathroom, and after handling raw meat or poultry. Clean kitchen surfaces, utensils, and cutting boards by washing them with hot, soapy water.
  • To prevent cross-contamination, use separate cutting boards and utensils for raw meat, poultry, seafood, and vegetables. Store raw meat and poultry on the bottom shelf of the refrigerator to avoid drips onto other foods.
  • Avoid raw or undercooked eggs, meat, and seafood. A food thermometer ensures that meat, poultry, fish, and eggs are cooked to safe internal temperatures. This helps kill harmful bacteria. Follow recommended cooking temperatures for different types of food.
  • Refrigerate perishable foods promptly, ideally within two hours of purchase or preparation. Keep the refrigerator temperature at or below 40°F. 


Why Food Poisoning May Be Related To Your Digestive Symptoms

Recognizing the transition from acute food poisoning to chronic digestive symptoms is crucial for understanding the potential long-term effects of AGE on gastrointestinal health. While acute symptoms may resolve, chronic issues can persist, emphasizing the need for proactive management. Individuals experiencing prolonged digestive symptoms post-food poisoning are encouraged to consult healthcare professionals for personalized guidance. Managing the long-term effects of food poisoning involves adopting a comprehensive approach, including dietary adjustments, lifestyle modifications, and potential medical interventions. By addressing these issues early and seeking professional advice, individuals can optimize their digestive health and mitigate the impact of lingering symptoms, ensuring a more sustained and robust recovery.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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