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You’re eating more vegetables, increasing your fiber, incorporating fermented foods, and making healthier choices. But by the afternoon, your stomach is so bloated that you’re uncomfortable in your own clothes. Sound familiar?

Persistent bloating despite eating healthy can be incredibly frustrating, especially when you’re doing everything you think you should to support your gut health. But what if the solution isn’t another restrictive diet or cutting out even more foods?

In this episode, Brigid explores the underlying causes of bloating and digestive discomfort that may persist even after you’ve improved your nutrition. Drawing on over a decade of clinical experience and thousands of comprehensive stool tests, Brigid explains how imbalances in the gut microbiome, small intestinal bacterial overgrowth (SIBO), increased intestinal permeability, inflammation, and digestive enzyme dysfunction may contribute to ongoing symptoms.

She also discusses the connection between gut health, hormones, chronic stress, and inflammation, along with the role of functional medicine testing and personalized nutrition coaching in identifying potential root causes. Most importantly, you’ll learn why the goal of improving gut health isn’t to eliminate every food that causes discomfort. It’s to build a healthier, more resilient digestive system that allows you to enjoy a greater variety of nutrient-dense foods.

What You’ll Learn In This Episode:

• Why eating healthy doesn’t always eliminate bloating, gas, or digestive discomfort.
• Six potential root causes of persistent bloating and gut microbiome imbalances.
• How to recognize digestive and whole-body symptoms that may indicate underlying gut dysfunction.
• The connection between SIBO, leaky gut, inflammation, and digestive health.
• How antibiotics, medications, sugar, alcohol, and chronic stress may affect your gut microbiome.
• Why hormonal shifts during pregnancy, postpartum, perimenopause, and menopause matter for gut health.
• When conventional testing, SIBO breath testing, or comprehensive stool testing may be appropriate.
• How the functional medicine 5R framework can help guide individualized gut health strategies.
• Why an anti-inflammatory diet, consistency, and food diversity remain foundational for long-term gut health.

Timestamps:

• 00:00 Why bloating can persist despite gut-friendly changes
• 02:17 A healthy gut means tolerating more foods
• 03:43 Gut symptoms and whole-body warning signs
• 05:04 When to try the basics and when to call your doctor
• 06:30 Brigid’s personal experience with gut symptoms
• 07:54 Six possible underlying causes of ongoing GI issues
• 10:32 Everyday contributors: medications, diet, and stress
• 16:49 Pregnancy, postpartum, and menopause-related shifts
• 18:36 Conventional, breath, and stool testing explained
• 21:20 The five R framework for gut support
• 23:07 Build food tolerance and avoid testing before the basics
• 24:49 How quickly diet can influence the gut microbiome

Why Am I Still Bloated Even Though I Eat Healthy?

If you’ve already increased your fiber intake, started eating more vegetables, incorporated fermented foods, and focused on hydration, you might expect your digestive symptoms to improve. And for many people, they do.

A consistent, fiber-rich, anti-inflammatory diet can help support beneficial gut bacteria, improve bowel regularity, and promote a healthier gut microbiome. But when bloating, gas, abdominal distension, or irregular bowel movements continue despite these changes, there may be additional factors contributing to your symptoms.

Brigid explains that digestive symptoms should be viewed as information rather than something to simply tolerate or ignore. Common digestive signs include frequent bloating, excess gas, reflux, irregular bowel movements, and new difficulties tolerating foods that previously caused no issues. Gut health imbalances may also be associated with symptoms outside the digestive system, including fatigue, brain fog, skin concerns, and joint discomfort.

The important distinction is that these symptoms don’t automatically mean you need expensive functional medicine testing. First, it’s essential to evaluate your current nutrition habits, lifestyle, and medical history. If you’ve already established a consistent foundation and your symptoms persist, that’s when a deeper evaluation may become more meaningful.

Six Potential Root Causes of Persistent Bloating

One of the most important lessons in functional nutrition is that similar symptoms can have very different underlying causes. Two women may both experience daily bloating, but the factors contributing to their digestive discomfort may be entirely different.

In this episode, Brigid highlights six potential contributors to persistent bloating.

1. Too Few Beneficial Gut Bacteria

A healthy gut microbiome depends on having enough beneficial bacteria, including strains of Lactobacillus and Bifidobacterium. These microorganisms help support digestive function, microbial balance, and the production of beneficial compounds. When populations of helpful bacteria are reduced, digestive symptoms may become more noticeable.

Brigid also cautions against unnecessary use of antimicrobials or supplements like berberine without professional guidance, because the goal isn’t simply to eliminate bacteria. It’s to support a healthy microbial ecosystem.

2. Small Intestinal Bacterial Overgrowth (SIBO)

SIBO occurs when excessive bacteria are present in the small intestine. These bacteria can ferment carbohydrates and produce gas, contributing to symptoms such as bloating, abdominal discomfort, distension, flatulence, and diarrhea.

Bloating is one of the most commonly reported symptoms. Because a stool test primarily evaluates what’s happening in the large intestine, it cannot diagnose SIBO. Breath testing is one method healthcare providers may use when evaluating suspected small intestinal bacterial overgrowth.

3. Increased Intestinal Permeability (Leaky Gut)

Increased intestinal permeability, commonly called leaky gut, refers to changes in the intestinal barrier that can allow substances to pass through the intestinal lining more readily. Brigid shares her own experience with severe digestive symptoms, fatigue, neurological concerns, and acne during her teenage years.

Working with a functional medicine practitioner helped her explore intestinal permeability and develop an individualized nutrition and supplement protocol. Her experience ultimately influenced her career in functional nutrition and her approach to identifying potential contributors to digestive dysfunction. While intestinal permeability is an active area of research, it is important to recognize that symptoms alone cannot establish a diagnosis.

4. Gut Inflammation

Inflammation in the digestive tract is another factor worth evaluating when symptoms persist.

Brigid discusses stool markers such as calprotectin, secretory IgA, and eosinophil protein X (EPX), which may provide different types of information about intestinal inflammation and immune activity.

These markers require clinical interpretation and are not interchangeable measures of inflammation. Understanding whether inflammation is present can help guide the next steps in a personalized gut health evaluation.

5. Low Digestive Enzyme Production or Stomach Acid

Digestive enzymes help break down food so that nutrients can be absorbed. When digestive enzyme production is inadequate, more undigested food may reach intestinal bacteria, where fermentation can contribute to gas and bloating.

However, that doesn’t mean everyone experiencing digestive discomfort needs a digestive enzyme supplement. Brigid emphasizes the importance of identifying whether additional digestive support is actually needed instead of guessing.

6. Low Short-Chain Fatty Acid Production

Short-chain fatty acids are beneficial compounds produced when gut bacteria ferment certain types of dietary fiber. One particularly important short-chain fatty acid is butyrate, which provides energy to cells lining the colon. Adequate short-chain fatty acid production helps support intestinal health and is one reason fiber-rich foods are so valuable for the gut microbiome.

Rather than permanently eliminating fiber-containing foods, the long-term goal is to support a digestive environment that can better tolerate them.

How Medications, Stress, and Lifestyle Factors Impact Gut Health

Even women who prioritize their nutrition can experience changes in their gut microbiome.

Brigid explains that gut health is influenced by far more than the foods on your plate. Antibiotic exposure, for example, can alter microbial composition and diversity. While antibiotics are sometimes essential and lifesaving, research suggests that some microbiome changes can persist long after treatment.

The episode also discusses Saccharomyces boulardii, a probiotic yeast studied for its potential to reduce antibiotic-associated diarrhea in certain populations. Whether probiotic supplementation is appropriate depends on the individual and should be discussed with a healthcare professional.

Other potential contributors include frequent use of nonsteroidal anti-inflammatory drugs (NSAIDs), acid-reducing medications such as proton pump inhibitors, high intakes of added sugar and refined carbohydrates, and alcohol consumption. Brigid emphasizes that prescribed medications should never be discontinued without guidance from the prescribing clinician.

The Gut-Brain Connection: Why Chronic Stress Matters

One of the most overlooked components of gut health is chronic stress. The digestive system and nervous system communicate through the gut-brain axis, which helps regulate digestion, intestinal function, and responses to stress. Research suggests that psychological stress can influence intestinal permeability and digestive symptoms.

Brigid discusses how some people pursue increasingly restrictive diets, supplements, and testing protocols while overlooking the impact of ongoing stress. Supporting gut health may also mean prioritizing sleep, slowing down during meals, and developing strategies that help regulate the nervous system. A holistic nutrition approach considers not only what you’re eating but also the environment in which you’re eating and the stress your body is experiencing.

Gut Health and Hormones: Pregnancy, Perimenopause, and Menopause

Women’s health and hormone health are closely connected with changes in the gut microbiome throughout different stages of life. Pregnancy and postpartum recovery can involve significant hormonal and microbial shifts. Changes in medications, sleep, stress, and digestive patterns during this period may also influence gut health.

Perimenopause and menopause bring additional changes. Brigid highlights research suggesting that postmenopausal women may have different gut microbiome compositions and lower microbial diversity compared with premenopausal women. These findings help explain why gut health deserves attention as part of a broader approach to women’s nutrition and healthy aging.

Supporting gut health during perimenopause and menopause may involve maintaining a fiber-rich diet, consuming a variety of plant foods, prioritizing sleep, and addressing persistent digestive symptoms with a qualified healthcare professional. For a deeper discussion of the connection between hormonal changes, gut health, and inflammation, Brigid recommends her previous episode with Cynthia Thurlow about leaky gut, brain fog, and autoimmune risk in menopause.

When Should You Consider Gut Health Testing?

If you’ve consistently improved your nutrition and lifestyle but continue experiencing digestive symptoms, additional testing may be appropriate. However, Brigid makes an important distinction: testing should be guided by your symptoms and clinical history, not simply by the desire for more data.

When Should You Consider Gut Health Testing?

If you’ve consistently improved your nutrition and lifestyle but continue experiencing digestive symptoms, additional testing may be appropriate. However, Brigid makes an important distinction: testing should be guided by your symptoms and clinical history, not simply by the desire for more data.

1. Conventional Digestive Testing

A healthcare provider may first evaluate common conditions that can contribute to digestive discomfort, including:

• Celiac disease
• Lactose intolerance
• H. pylori infection
• Thyroid dysfunction
• Iron deficiency or anemia
• Vitamin B12 deficiency

Celiac disease testing is especially important to discuss before removing gluten, because eliminating gluten beforehand can affect the accuracy of testing.

2. SIBO Breath Testing

When symptoms suggest small intestinal bacterial overgrowth, a healthcare provider may consider breath testing. This is different from stool testing because it is designed to evaluate gas production associated with bacterial activity in the small intestine.

3. Comprehensive Stool Testing

Brigid also discusses comprehensive stool tests, including GI Effects by Genova Diagnostics and GI-MAP by Diagnostic Solutions. Depending on the test, these panels may include markers related to digestive function, inflammation, microbial composition, short-chain fatty acids, and other aspects of intestinal health.

However, not every commercial stool microbiome marker has established clinical usefulness, and results should not be interpreted as definitive diagnoses on their own. Brigid encourages working with an experienced practitioner who can consider test findings alongside symptoms, medical history, and nutrition patterns.

The Functional Medicine 5R Framework for Gut Health

Rather than relying on a one-size-fits-all elimination diet, Brigid describes the functional medicine 5R framework for approaching gut health.

1. Remove: Identify and address potential triggers, infections, or overgrowths when clinically appropriate. Temporary dietary changes may be considered based on individual needs.
2. Replace: Evaluate whether digestive support, such as pancreatic enzymes, is needed.
3. Reinoculate: Support beneficial microorganisms through appropriate dietary strategies, fermented foods, or targeted probiotics when indicated.
4. Repair: Provide nutrients and dietary support that help maintain a healthy intestinal barrier, including adequate protein and beneficial fats.
5. Rebalance: Address the broader lifestyle factors that influence digestive health, including stress, sleep, meal timing, and nervous system regulation.

The 5R framework provides a way to organize individualized care, but the specific interventions should be guided by clinical findings rather than applied as a universal protocol.

Why the Goal Is to Eat More Foods, Not Fewer

One of Brigid’s biggest messages in this episode is that long-term gut health shouldn’t be defined by an ever-growing list of foods you can’t eat. Foods like beans, lentils, vegetables, and other fiber-rich plant foods provide valuable nutrients and compounds that support the gut microbiome. They also play an important role in blood sugar balance, insulin sensitivity, cardiovascular health, and an anti-inflammatory eating pattern.

When someone experiences digestive discomfort after eating these foods, the answer isn’t necessarily to eliminate them forever. Instead, it’s important to understand why they’re causing symptoms and whether an individualized strategy could improve tolerance over time. This is where functional nutrition, personalized nutrition coaching, and consistent dietary habits can be valuable. The goal is to use food as medicine in a sustainable way rather than pursuing perfection or unnecessary restriction.

Final Takeaway: Listen to Your Gut Before Eliminating More Foods

If you’re eating healthy but still struggling with bloating, the next step isn’t automatically another supplement, elimination diet, or expensive stool test. Start by evaluating your nutrition and lifestyle foundations. Consider whether your symptoms have improved with consistent dietary changes, and pay attention to patterns that may indicate a need for further evaluation.

If digestive symptoms persist, work with a qualified healthcare professional to explore potential causes and determine whether testing is appropriate. Seek medical evaluation promptly for concerning symptoms such as blood in the stool, unexplained weight loss, anemia, or symptoms that wake you from sleep.

A healthier gut isn’t necessarily one that tolerates fewer foods. For many people, it’s one that can comfortably handle a greater diversity of nourishing foods while supporting long-term metabolic health, hormone health, and overall well-being. The goal isn’t to eat less. It’s to understand your body, address what’s contributing to your symptoms, and create a sustainable foundation for better gut health.

Resources & Links:

+ Watch the full episode on YouTube

+ Join The Being Collective
+ Brigid’s Website
+ Brigid’s Instagram

Enjoyed this episode? Follow The BeingBrigid Show, leave a rating or review, and share it with a friend who’s been struggling with digestive symptoms despite eating healthy.

For more science-backed strategies on gut health, blood sugar balance, inflammation, and women’s nutrition, explore our other episodes and nutrition resources.