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Understanding What Causes Gut Health Issues: A Comprehensive Guide

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Published By: Dr. Jeffrey Mark
Date: June 13, 2024

Gut health is a critical component of overall well-being, impacting everything from digestion to mental health. Understanding the causes of gut health issues is essential for effective prevention and treatment. This comprehensive guide explores the various factors that can lead to gut health problems, including the role of gut microbiota, dietary factors, medications, environmental influences, and the gut-brain axis.

Case Study

Robert came to see us regarding several gut issues including heartburn, bloating after eating, and constipation. He has had problems with heartburn and reflux ever since his 20s and has been taking Prilosec (a proton pump inhibitor or PPI) daily for over 20 years now at age 47. He was also taking Advil at least 3 times a week for aches and pains after golfing and for headaches. 

He had problems falling asleep and felt tired even after “seven hours” of sleep.   He has had routine medical care and gastroenterology evaluations including basic lab chemistries, a breath test for Helicobacter pylori, an upper endoscopy,  a colonoscopy, and abdominal ultrasound, all of which were unremarkable. 

We did additional studies on Robert including a map of his entire microbiome, placed him on an elimination diet and ordered food sensitivity testing, ordered a breath test for small intestinal bacterial overgrowth, measured his hormones including a 4 point salivary cortisol test, and had him undergo a sleep study. 

He was found to have dysbiosis or an imbalance in his microbiome with more inflammatory bacteria, intestinal permeability (“Leaky gut”), food sensitivities (wheat, walnuts, egg whites, corn, catfish, shellfish),  small intestinal bacterial overgrowth, stage 2 adrenal stress, and sleep apnea.  

We addressed his gut health as the root cause of his problems. The first step was to remove the foods he was sensitive to, increase water consumption, and use magnesium products to get daily bowel movements. A diet restricting easily fermentable carbohydrates (low FODMAP diet), and using nutraceuticals (supplements with “medicinal” like properties beyond their nutritional value) to promote healing of the gut lining, increase motility, improve digestion, and remove the small bowel bacterial overgrowth was then initiated.

Adaptogens to balance his cortisol, a phone app for meditation, a CPAP machine,  and lifestyle changes helped with stress and sleep. A detoxification, exercise,  and weight program including intermittent fasting helped him lose weight, and wean off the Prilosec and Advil.  He currently does not have heartburn, eats without bloating, and has regular bowel movements.

Key Takeaways

  • Gut microbiota play a crucial role in maintaining overall health, and imbalances can lead to various diseases.
  • Dietary choices, such as high-sugar and high-fat diets, artificial additives, and food allergens, significantly impact gut health.
  • Medications like antibiotics, NSAIDs, and PPIs can disrupt the gut microbiome, leading to health issues.
  • Environmental factors and lifestyle choices, including stress, sleep deprivation, and physical activity, influence gut health.
  • The gut-brain axis highlights the connection between mental health and gut health, emphasizing the importance of a balanced microbiome.

The Role of Gut Microbiota in Health and Disease

Microbiota in Health and Disease

Composition of Gut Microbiota

The gut microbiota is a complex community of microorganisms residing in the gastrointestinal tract. This community includes bacteria, viruses, fungi, and other microbes. The composition of gut microbiota varies significantly among individuals and is influenced by factors such as diet, age, genetics, and environment.

A balanced gut microbiota is essential for maintaining overall health. Disruptions in this balance can lead to various health issues, including intestinal disorders, metabolic diseases, and even mental health conditions.

Functions of Gut Microbiota

The gut microbiota performs several critical functions in the body:

  • Digestion and Absorption: It aids in the ingestion of complex carbohydrates and the absorption of nutrients.
  • Immune System Regulation: The gut microbiota plays a role in regulating the immune system, helping to protect against pathogens and prevent autoimmune disorders.
  • Production of Metabolites: The microbiota produces essential metabolites, such as short-chain fatty acids, which have anti-inflammatory properties.
  • Brain Health: The gut microbiota influences brain function by producing neurotransmitters like serotonin and GABA, which can affect mood and cognitive functions.

Impact of Dysbiosis on Health

Dysbiosis refers to an imbalance in the gut microbiota, where harmful bacteria outnumber beneficial ones. This imbalance can lead to increased gut permeability, often referred to as leaky gut, allowing toxins and pathogens to enter the bloodstream. Dysbiosis has been linked to a range of health issues, including inflammatory bowel disease, obesity, diabetes, and even neurological conditions like Alzheimer's and Parkinson's disease.

Understanding the role of gut microbiota in health and disease is crucial for developing effective therapeutic interventions. By maintaining a healthy gut microbiota, we can potentially prevent and manage various health conditions.

Dietary Factors Contributing to Gut Health Issues

Dietary Factors Contributing to Gut Health Issues

High-Sugar and High-Fat Diets

Highly processed foods, often characterized by their low fiber content high levels of sugar, and unhealthy fats, can significantly harm intestinal health. These types of foods may contribute to an imbalance in the gut microbiome, known as dysbiosis. Such an imbalance can weaken the intestinal barrier, making it more permeable and susceptible to leaky gut syndrome. Gut health issues that cause weight gain are often linked to these dietary patterns.

Artificial Additives and Preservatives

Certain additives found in processed foods, such as emulsifiers, preservatives, and artificial sweeteners, have been shown to interfere with the gut's natural function. These substances can irritate the gut lining, further exacerbating the condition. A diet lacking in fermented foods, which are rich in probiotics, can lead to a reduction in beneficial gut bacteria.

Food Allergens and Sensitivities

Food allergens and sensitivities, such as those to gluten or dairy, can trigger inflammatory responses in the gut. This tenderness can damage the gut lining and contribute to increased intestinal permeability. Avoiding food allergens and processed foods can improve intestinal health.

Adopting a "leaky gut diet" rich in fruits, vegetables, and fermented foods while avoiding food allergens and processed foods can improve intestinal health.

Impact of Medications on Gut Health


Medications can have profound effects on gut health, often leading to significant changes in the gut microbiome and overall intestinal function. Understanding these impacts is crucial for managing and mitigating potential adverse effects on intestinal health.

Antibiotics and Gut Flora

Antibiotics are well-known for their ability to save lives by combating bacterial infections. However, they can also disrupt the delicate balance of the gut microbiome. Antibiotics can lead to a reduction in beneficial bacteria, paving the way for bad bacteria to proliferate. This imbalance, known as dysbiosis, can result in various intestinal issues, including diarrhea and increased gut permeability.

Non-steroidal Anti-inflammatory Drugs (NSAIDs)

NSAIDs, commonly used for pain relief and pain reduction, can also negatively impact intestinal health. These medications can cause irritation of the gut lining, leading to ulcers and bleeding. Moreover, NSAIDs have been connected to intestinal bacteria imbalances that cause increased gut permeability, often referred to as "leaky gut." This condition can trigger systemic inflammation and contribute to various health issues.

Proton Pump Inhibitors (PPIs)

Proton Pump Inhibitors, used to treat acid-related disorders, can also affect the gut microbiome. Long-term use of PPIs has been associated with changes in the gut microbiome, potentially leading to dysbiosis. Additionally, PPIs can reduce the stomach's acidity, which is essential for killing bad bacteria and aiding absorption. This reduction in acidity can allow pathogenic bacteria to thrive, further disrupting intestinal health.

The interplay between medications and intestinal health underscores the importance of considering the gastrointestinal effects when prescribing and using these drugs. Careful management and monitoring can help mitigate adverse outcomes and support overall intestinal health.

Environmental and Lifestyle Influences on Gut Health

improve gut health

Stress and Gut Function

Stress has a profound impact on gut health. It can alter gut motility, increase gut permeability, and affect the balance of gut microbiota. Chronic stress can lead to a condition known as "leaky gut," where the intestinal barrier becomes compromised, allowing harmful substances to enter the bloodstream. This can trigger tenderness and contribute to various health issues.

Sleep Deprivation and Gut Health

Adequate sleep is essential for maintaining good health. Sleep deprivation can disrupt the circadian rhythm, which in turn affects the gut microbiome. Studies have shown that poor sleep quality is associated with a decrease in beneficial gut bacteria and an increase in bad bacteria. This imbalance can lead to digestive issues and systemic inflammation.

Physical Activity and Gut Microbiome

Regular physical activity is beneficial for gut health. Exercise can increase the diversity of gut microbiota, which is crucial for overall health. It also helps in regulating bowel movements and reducing inflammation. Incorporating moderate exercise into your daily routine can have a positive impact on your intestinal health.

Understanding the intricate relationship between lifestyle factors and intestinal health is essential for developing effective strategies for preserving gut health. This comprehensive guide on intestinal health by a gastroenterologist covers the gut-brain connection, common gut issues, healing actions, lifestyle practices, and gut microbiome importance. It emphasizes holistic well-being and practical strategies.

The Gut-Brain Axis: How Mental Health Affects Gut Health

Mechanisms of the Gut-Brain Connection

The gut is often referred to as the "second brain" due to its extensive network of nerves and its ability to produce neurotransmitters. This connection is facilitated by the enteric nervous system (ENS), which communicates with the central nervous system (CNS) through the vagus nerve.

The gut microbiome may affect brain health by producing brain chemicals and communicating with nerves that connect to the brain. For instance, serotonin, an antidepressant neurotransmitter, is predominantly produced in the gut.

Impact of Stress and Anxiety

Stress and anxiety can significantly impact intestinal health. The gut-brain axis allows for bidirectional communication, meaning that stress can lead to gastrointestinal issues, and gut problems can exacerbate stress and anxiety. This is why people often experience gastrointestinal distress during periods of high stress. The gut microbiome may also affect brain health by helping control the messages that are sent to the brain through these nerves.

Role of Probiotics in Mental Health

Certain probiotics have been shown to improve symptoms of depression and other mental health disorders. These beneficial bacteria can help maintain a healthy balance in the gut microbiome, which is crucial for both physical and mental health. Probiotics may also produce neurotransmitters like serotonin and GABA, which can influence mood and mental well-being.

Optimizing the gut-brain axis is critical to your mental health. Keeping the good and bad bugs in proper balance is essential to your mental health.

Common Symptoms and Clinical Manifestations of Intestinal Health Issues

Intestinal health issues can manifest in a variety of symptoms that affect not only the digestive system but also other parts of the body. Understanding these symptoms is crucial for early detection and management of gut-related disorders.

Effective Therapeutic Interventions for Gut Health

Dietary Modifications

Dietary changes are fundamental to improving gut health. Adopting a diet rich in fruits, vegetables, and fermented foods while avoiding food allergens and processed foods can significantly enhance gut function. Eliminating potential triggers such as sugar, gluten, and dairy is often recommended. Additionally, incorporating bone broth, which is rich in collagen and amino acids, can help repair the gut lining.

Probiotic and Prebiotic Supplementation

Probiotics and prebiotics play a crucial role to maintain a healthy gut microbiome. Probiotics, found in fermented foods like sauerkraut and kimchi, introduce beneficial bacteria into the gut. Prebiotics, found in fiber-rich foods such as onions and garlic, feed these beneficial bacteria. A comprehensive guide by a gastroenterologist on gut health often emphasizes the importance of these supplements for a thriving gut microbiome. 

Maintaining a diverse array of bacteria in the gut is crucial for good health. Good bacteria, such as Lactobacillus and Bifidobacterium, play a vital role in maintaining the balance of bacteria in the gut. An imbalance in gut bacteria, characterized by an overgrowth of harmful microbes, can lead to various health issues, underscoring the importance of cultivating a good balance of bacteria for overall well-being.

Lifestyle Changes

Lifestyle modifications are equally important in managing intestinal health. Stress management techniques, regular physical activity, and adequate sleep are essential components. Stress can negatively impact gut function, so incorporating relaxation techniques such as meditation and yoga can be beneficial. Furthermore, regular exercise and sufficient sleep contribute to overall intestinal health by promoting a balanced microbiome and reducing inflammation.

A comprehensive approach to intestinal health involves not only dietary and supplemental interventions but also significant lifestyle changes. Addressing stress, sleep, and physical activity can create a holistic environment for gut healing and maintenance.

Effective therapeutic interventions for intestinal health can significantly improve your overall well-being. At The Real Gut Doctor, we specialize in personalized care that addresses the root causes of your digestive issues. Our comprehensive approach includes tailored dietary plans, specialized supplements, and lifestyle adjustments to help you regain your energy and vitality. Ready to take the first step towards better health? Visit us to learn more and schedule a discovery call today!


Understanding the causes of intestinal health issues is crucial for maintaining overall well-being. The gut, often referred to as the second brain, plays a pivotal role in various bodily functions, including digestion, immune response, and even mental health.

Factors such as diet, stress, medications, and environmental toxins can significantly impact intestinal health, leading to conditions like leaky gut syndrome and dysbiosis. Effective therapeutic interventions, including dietary modifications, stress management, and the use of probiotics and prebiotics, can help restore and ensure a healthy gut microbiome.

By prioritizing intestinal health, individuals can improve not only their digestive health but also their overall physical and mental health. This comprehensive guide underscores the importance of a holistic approach to intestinal health, emphasizing the need for personalized and multifaceted strategies to address and prevent gut-related issues.

Frequently Asked Questions

Why Is Gut Health Important?

Gut health is crucial because the gut is involved in essential bodily functions such as absorption, nutrient absorption, and immune system support. It also has a significant impact on mental health through the gut-brain axis.

What Are Common Symptoms Of Gut Health Issues?

Symptoms that are common include digestive problems like bloating, constipation, and diarrhea, as well as systemic issues like fatigue, skin irritation, and even neurological symptoms such as brain fog and anxiety.

How Does Diet Affect Gut Health?

Diet plays a significant role in gut health. High-sugar and high-fat diets, artificial additives, preservatives, and food allergens can disrupt the balance of gut microbiota, leading to issues like dysbiosis and increased gut permeability.

Can Medications Impact Gut Health?

Yes, medications such as antibiotics, NSAIDs, and proton pump inhibitors can negatively affect gut health by altering the composition of gut microbiota and increasing gut permeability.

What Lifestyle Changes Can Improve Gut Health?

Effective lifestyle changes include managing stress, getting adequate sleep, engaging in regular physical activity, and consuming a balanced diet rich in fiber, probiotics, and prebiotics.

How Is The Gut Connected To Mental Health?

The gut-brain axis is a bidirectional communication system between the gut and brain. Imbalances in gut microbiota can affect mental health, potentially leading to conditions like anxiety and depression. Probiotics may help in maintaining mental well-being.

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Dr. Jeffrey Mark
With over thirty years of experience, Dr. Mark is a leading expert in holistic gut health. His integrative approach combines conventional medicine, functional and regenerative medicine, and advanced therapies to heal the gut and transform patient health. Holding 5 board certifications, Dr. Mark offers the comprehensive expertise of five medical specialists during each patient visit. He is dedicated to optimizing wellbeing by addressing the gut-related root causes of chronic health issues.
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