If you struggle with constipation, you know how discouraging it can be when you’re doing everything right: eating your vegetables, drinking more water, and taking fiber supplements, but nothing seems to work. Frustrating, isn’t it?
While diet is important, it’s not always enough. Sometimes constipation is caused by hidden factors that diet alone can’t address.
Prefer to watch? Here’s the video version of this post.
One key factor is gut motility, the rate at which food moves through the digestive tract. Slow motility results in constipation. Motility can be affected by several things, including your gut microbiome, inflammation from food sensitivities, and overgrowths of harmful microbes in the small intestine.
In this post, I’ll walk you through the five surprising causes of constipation I see most often in my clinical practice. And I’ll share what you can actually do about them.
1. Methane-Dominant SIBO
Sometimes constipation isn’t just about what you eat; it’s about what’s happening in your small intestine. Unlike the large intestine, which houses most of your gut bacteria, the small intestine is primarily responsible for nutrient absorption and usually contains very few microbes.
Your small intestine is kept relatively free of bacteria and food debris by a cleansing wave known as the Migrating Motor Complex (MMC). This wave sweeps through your small intestine every 90 minutes between meals and repeatedly overnight while you sleep.
However, the nerve cells that trigger this cleansing wave can be damaged after a food poisoning incident or infection from pathogens like Giardia. When the MMC doesn’t function correctly, bacteria can overgrow in the small intestine, leading to a condition known as Small Intestinal Bacterial Overgrowth (SIBO).
If the overgrown bacteria are methane-producing, digestion slows significantly, leading to constipation. That’s why, even if you eat plenty of fiber or take probiotics, you can still be constipated.
What you can do: A 3-hour lactulose breath test can reveal if methane-dominant SIBO is the culprit. Once identified, your treatment plan needs to include targeted antimicrobials and other strategies to clear the methanogen overgrowth, stimulate the nerves of the MCC, and restore balance to optimize motility.
2. Intestinal Methanogen Overgrowth (IMO)
Methane-producing microbes can overgrow in either the small or large intestine. When this happens in the small intestine, it’s called methane-dominant SIBO (as we discussed earlier). When it occurs in the large intestine only, it’s referred to as Intestinal Methanogen Overgrowth (IMO).
Unlike SIBO, IMO isn’t caused by a problem with the Migrating Motor Complex. Instead, it’s often linked to an imbalanced microbiome and a high stool pH, which creates the perfect conditions for methane-producing microbes to thrive.
Regardless of where methane is produced (whether in the small or large intestine), it slows gut motility, resulting in constipation. This is why some people can eat a healthy diet and still struggle with constipation.
What you can do: Advanced microbiome testing using Whole Genome Sequencing can measure the percentage of methane-producing archaea and how much methane is being produced. This helps pinpoint whether IMO is your root cause. This type of microbiome testing is accurate, cost-effective, and a critical first step for creating a targeted plan to restore healthy motility. Avoid older tests, such as the GI Map, which rely on outdated technology and are less reliable.
In my free Constipation Relief guide, I discuss specific options for this type of test and provide more details on where to obtain it. You can download that guide here.
3. Fungal Overgrowth in the Gut (Candida & Yeast)
Constipation can also be caused by fungal overgrowth in the small or large intestine. When it occurs in the small intestine, it’s called SIFO (Small Intestinal Fungal Overgrowth). Overgrowth of fungi, such as Candida or other yeasts, can slow gut motility and lead to bloating, constipation, cravings for sugar, carbs, or alcohol, brain fog, and even weight gain.
A common trigger for fungal overgrowth is the use of antibiotics, which can kill beneficial bacteria and allow yeast to flourish. Other medications, including prednisone, oral estrogen (birth control), and certain immunosuppressing drugs, can also worsen fungal growth. Diets high in sugar or refined carbohydrates further fuel yeast, creating an ideal environment for overgrowth.
What you can do: Advanced microbiome testing can identify fungal overgrowth and determine which species are present. Once identified, a targeted approach that includes natural antifungal therapies in combination with a diet low in refined sugar and simple carbs can help restore balance, improve motility, and relieve constipation while supporting weight loss.
4. Food Sensitivities & Gut Inflammation
Constipation can sometimes be caused not by what you eat, but by how your body reacts to certain foods. Common culprits include dairy, gluten, eggs, and soy, which can trigger inflammation in the gut lining and slow intestinal motility.
Here’s how it works: when your immune system reacts to a food you’re sensitive to, it releases inflammatory mediators in the gut. These chemicals can disrupt the smooth muscle contractions required for normal bowel movements, slowing digestion and contributing to constipation.
Unlike food allergies, which cause immediate reactions, food sensitivities are often delayed. You might not notice symptoms until hours or even days after eating, making it hard to connect a specific food to bloating or constipation. This is why many people remain frustrated despite eating “healthy” foods.
Signs that food sensitivities may be affecting your constipation:
What you can do: Advanced testing, such as Mediator Release Testing (MRT) or an elimination diet, can identify which foods trigger inflammation. Once identified, removing these foods for 6 weeks to 6 months, depending on the severity of the reaction, can help calm inflammation, restore normal motility, and relieve constipation.
5. Butyrate and Your Microbiome
Your gut microbiome plays a crucial role in digestion, and one of the key players in maintaining healthy motility is butyrate, a short-chain fatty acid produced by beneficial gut bacteria. Butyrate helps nourish the cells of your colon, supports anti-inflammatory processes, and stimulates smooth muscle contractions needed for regular bowel movements.
When your microbiome is imbalanced due to a poor diet, antibiotics, or overgrowth of harmful microbes, butyrate production can decrease. Without enough butyrate, the colon becomes less efficient at moving stool along, which can lead to sluggish digestion and constipation.
Low butyrate can also contribute to Visceral Hypersensitivity, a condition where the nerves in your gut become inflamed. This makes even small amounts of gas feel painful. Butyrate helps calm this inflammation, relieving bloating, cramping, and discomfort.
Signs that low butyrate may be contributing to constipation:
- Bloating
- Abdominal pain or discomfort in the lower abdomen
- Trapped gas (butyrate enhances motility and relieves trapped gas)
What you can do: Supporting butyrate production involves:
- Following a Mediterranean-style diet rich in fruits, vegetables, beans, and resistant starches.
- If you can tolerate them, aim for around 15 grams of resistant starch daily to support butyrate production.
- If these foods cause symptoms, it could be a sign that another underlying issue, such as SIBO, IMO, fungal overgrowth, or food sensitivities, is contributing to your constipation and needs to be addressed first.
Next Steps
Constipation can feel frustrating and confusing, especially when you’re doing “all the right things” yet still not seeing results. The truth is, there’s almost always a deeper reason motility is slow. Once you uncover your unique root cause, things can finally shift.
To help you get started, I created a Constipation Relief Guide. It guides you through advanced testing options, key strategies, and straightforward steps you can take today for lasting relief.