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Chronic Constipation? The Root Causes You Need to Know About

In this article, we are not going to be shy talking about our poop. In fact, it is probably the most important part of our digestive health, and may be the reason why you’re constantly bloated, fatigued, have acne and gas, and more. We’re going to review potential root causes of your constipation, the symptoms that follow, and holistic ways to diagnose and treat them.

*Please consult your doctor/practitioner with any serious symptoms and for proper diagnoses. Please use this as a guide and not for diagnosis/treatment options.


What Defines Chronic Constipation?

My IBS girlies, especially those with IBS-C or IBS-M, understand constipation all too well. If your stool is difficult to pass, hard and lumpy, and you have fewer than 3 bowel movements a week, you're chronically constipated.

And I don't have to break the news to you that not going to the bathroom daily is bad for the body. If we’re chronically constipated, stool basically ferments in our GI tract, causing toxins to be absorbed back into the body. Leading to even more bloat, gas, and digestive issues.

What may be more difficult to diagnose is the root cause of your constipation. I promise, it’s not the lack of fiber in your diet! In fact, you probably are following all of the basic rules for beating constipation, yet still suffer from it.

Most Basic Rules Ever for Beating Chronic Constipation

  1. Proper hydration, with electrolytes and minerals, to help movement of waste out of your body.

  2. Enough fiber (25 grams for women) to help bulk up stool. If you find that you need to increase your fiber intake, do it slowly or else you may experience more constipation/bloating. In addition to this, reducing sugar and ultra-processed foods that do not have nutritional value.

  3. Daily movement can help get your blood flowing and help with digestion, instead of being sedentary after a meal.

So, what do you do if you are following these guidelines and continue to have chronic constipation?

I can almost guarantee you that the answer is not in the form of a laxative or adding more fiber. These are things doctors prescribe as a way to alleviate temporary constipation, but they are not getting to the root issue. Instead, it’s time to look at the root cause of your chronic constipation/IBS.


Root Cause #1: Low Stomach Acid (Hydrochloric Acid)

Stomach acid is crucial for breaking down the food we consume, so nutrients can be absorbed by the small intestine and bloodstream. People believe that stomach acid is only an issue if they have high stomach acid, and present symptoms like acid reflux.

In reality, majority of people are struggling with low stomach acid, specifically when your body doesn’t produce enough hydrochloric acid (HCl).

Symptoms of Low Stomach Acid

We may present with low stomach acid if we have these symptoms almost immediately after we eat:

  • Constipation

  • Poor nutrient absorption of food (even on a healthy diet!)

  • Bloating

  • Gas

  • Feeling of fullness/lack of appetite

  • Low back pain

  • Fatigue

  • Headaches

  • Indigestion

Low stomach acid can also make us more susceptible to bacterial/yeast overgrowth like H. pylori, Candida overgrowth, and dysbiosis. Oftentimes, these microbes will be dissolved in stomach acid, but they pass through our GI tract if our stomach acid is too low.

Additionally, if food is not broken down all of the way, undigested particles of food can ferment in the GI tract, leading to Small Intestinal Bacterial Overgrowth (SIBO) and leaky gut.

Causes of Low Stomach Acid

You’ll find that with all of these root causes, there is oftentimes a series of diet/lifestyle choices that impair these functions. It’s not usually one singular cause (although it could be).

My low stomach acid was most likely due to chronic stress; an ultra-processed diet with lots of refined sugar, leading to chronic inflammation that altered my gut microbiome, and too much alcohol consumption in college.

In addition to this, you may find you have low stomach acid because of:

  • Overuse of protein pump inhibitors and antacids/acid-reducing medications, leading to lower production of HCl

  • H. pylori - common bacterial infection that can inhibit production of HCl

  • Autoimmune diseases

Diagnosis of Low Stomach Acid

While low stomach can be diagnosed in a clinical setting, I don't think it's worth going through the trouble. You have to swallow like a scope on the string to test the acidity in your stomach.

Instead, I worked with a naturopathic doctor who, through thoughtful consultations, reasoned my SIBO and dysbiosis could be due to low stomach acid.

If you want to try an at home test, you could do the baking soda test: Drink half a class of cold water combined with 1/4 teaspoon of baking soda on an empty stomach. This concoction should make you burp and if it takes you longer than 3-5 minutes to burp, you could have low stomach acid.

Treating Low Stomach Acid

As far as treating low stomach acid, you can incorporate digestive enzymes with Betaine HCl to increase HCl secretion before a meal. I take this supplement about fifteen minutes before I eat any meal.

You should also reduce processed foods, sticking to a whole foods based diet. Incorporate more fermented foods like sauerkraut, kimchi, and yogurt with your meals. You can also take diluted apple cider vinegar - 1 part ACV to 2 parts water - before your meal.

Lastly, stress management is helpful to overcoming low stomach acid. Stress can inhibit the secretion of gastric acids, including HCl. If you find that you are not salivating before a meal, have shortness of breath, or just feel generally anxious/uneasy, you may be too stressed to eat in the first place. Practicing mindful eating can initiate secretion of stomach acid.

Root Cause #2: Low Bile

Bile is a digestive fluid necessary for the digestion and absorption of fat and vitamins in the small intestine. It is formed in your liver and stored in your gallbladder and is mostly composed of water (95%) and bile acids/enzymes. Without it, we would not be able to properly break down the fat and cholesterol that we consume and eliminate waste.

When we don’t have enough bile, fat can build up and slow down our digestive system, causing constipation. And most of the bile that we produce is reabsorbed back into our liver. So, the more bile you secrete, the more that is stimulated. If it’s not secreted, then it is not reabsorbed, and that can lead to a slew of symptoms that mimic IBS.

Causes and Symptoms of Low Bile

Any impairment to your liver/gallbladder, including infection and inflammation, can lead to low bile secretion. Also, certain IBD like Chron’s and celiac disease can lead to low bile.

This leads to symptoms like:

  • Chronic constipation and/or watery diarrhea (IBS-M)

  • Greasy, foul smelling, and fatty stool that floats and is usually pale

  • Fatigue

  • Acid reflux/GERD

  • Jaundice (yellowing of the skin/eyes)

  • Gallstones

  • High cholesterol

  • Imbalance in the gut microbiome

  • Poor absorption of nutrients, like calcium and vitamin D

A nuclear medicine test called the SeHCAT, or a blood test testing for C4 enzyme levels can help diagnose low bile. Definitely work with your practitioner if you suspect you have low bile as a root cause of your constipation.

Treating Low Bile

There are holistic changes you can make to help with low bile secretion. Warm lemon juice on an empty stomach in the morning supports your liver's function and stimulates digestion. I incorporated this every morning and noticed a significant difference in my bowel habits: low bile production or not!

Inclusion of bitter foods like dandelion, fenugreek, turmeric, kale, arugula are said to stimulate bile production. Also, since the liver produces bile, liver-supportive foods like beets, radish, milk thistle, and cruciferous vegetables are beneficial.

Lastly, a shift to a low-fat, high-protein diet can help, incorporating only healthy fats like fish oil, avocado, nuts, olive oil as needed. And of course, a reduction in sugar and processed foods can promote healthy gut flora.

Root Cause #3: Dysbiosis

Dysbiosis is one of my root causes of chronic constipation, along with low stomach acid. It is a microbial imbalance within your gut microbiome. Basically, it means there is too much/too little of good and bad bacteria within your gut.

Dysbiosis can be found anywhere within your GI tract: From your stomach to your colon. But the imbalance of microbes can lead to digestive dysfunction - and it’s a delicate balance!

There are over trillions of microorganisms within our GI tract, and no two persons are the same. It is influenced by your genes, environment, diet, and lifestyle choices.

In fact, our microbiome begins the minute we are born, and depending on how we were birthed (vaginally or through a C-Section) can impact our gut microbiome today. Crazzzzzyyy!

Causes and Symptoms of Dysbiosis

Like these other root causes, it’s difficult to pinpoint a singular reason why you may have dysbiosis. A lot of factors can throw off someone’s microbiome.

For me, it was the overuse of antibiotics, a processed and refined-sugar rich diet (typical American diet), alcohol, and stress. All of this suppressed my immune system, leading to an overproduction of bad microbes and underproduction of healthy microbes.

Additionally, your immune system can be disrupted if you were exposed to mold or even viruses abroad (like traveler's diarrhea). Parasites can contribute to dysbiosis.

The imbalance in gut microbiota can worsen when there is an overgrowth of bacteria, like SIBO, or a yeast overgrowth like Candida. So, these can be both a cause and a symptom of dysbiosis, because a microbiome that cannot fight off parasites and bacteria, will allow more parasites and bacteria to come in. And the cycle continues…it’s so annoying.

Symptoms of dysbiosis are similar to those of IBS, including constipation, diarrhea, bloating, gas, stomach cramps. You can also have more physical and mental symptoms, like:

  • Brain Fog

  • Fatigue

  • Migraines

  • Acne

  • Joint pain

  • Sugar cravings

  • Yeast infections/oral thrush

  • Brittle nails

  • Depression/anxiety

  • Malnutrition

Diagnosing and Treating Dysbiosis

I would recommend different stool tests to show the type of dysbiosis you may have. I took one test recently - GI Map Diagnostic Solutions Kit from Direct Labs - which provided a panel of GI Markers, intestinal health, and survey of microbes, parasites, and fungi within my gut. It was very telling to the dysbiosis within my gut microbiome.

I also have done the Standard Process GI Panel a couple of years ago, which showed I had Candida Overgrowth I have since gotten rid of. You can work with a practitioner directly on the right stool test for you.

As far as treating dysbiosis, it can be a very unique protocol, since everyone’s microbiome is different. At baseline, it will probably be some type of "Removal, Repair, and Replenish” process. Again, what you incorporate for this process can be different for every individual.

Basic Overview of Dysbiosis Treatment

Phase One: Removal of Bad Bacteria

Based on the results of you GI Map, you could incorporate antimicrobials targeting the bad bacteria within your gut. Some forms of dysbiosis will benefit from antimicrobials with oregano, garlic, black walnut, or wormwood.

You can also incorporate diet and lifestyle modifications during this stage. You’ll most likely have to remove ultra-processed foods, sugars, and alcohol. It also may help to remove carbohydrates, like bread, pastas, rice, and potatoes. Once these carbohydrates are broken down into glucose, they can feed bad bacteria in our gut, making our symptoms worse. I have found it helpful to be on a low-sugar/low-carb diet. Also, remove poor lifestyle habits like chronic stress and lack of sleep.

Phase Two: Repair the Gut

Phase Three: Replenish your Gut Microbiome

Root Cause #4: Metabolic Dysfunction and Hormonal Imbalances

Metabolic dysfunction is a term thrown around a lot in holistic health. It’s the disruption of the body’s chemical processes, aka, metabolism. Metabolism is any reaction within the body that produces energy. It can be the synthesis of hormones, to the breakdown and conversion of food to energy within your gut.

Any change to metabolic processes can impact your overall health. A disruption to metabolic processes in your digestion, thyroid, liver, etc. can lead to an influx of illnesses and diseases.

Our gut microbiome can absolutely impact metabolic function within our body. Without the right makeup of bacteria, we cannot break down and synthesize important hormones and amino acids.

The most common types of metabolic disorders are insulin resistance (leading to prediabetes and Type II Diabetes) and hormonal imbalances (like hypo-/hyperthyroidism and PCOS).

Symptoms and Causes of Metabolic Disorders

It’s difficult to list all symptoms of metabolic disorders, because they can present themselves in different ways based on the type of dysfunction. However, IBS-like symptoms and chronic constipation can appear.

  • Symptoms of Insulin Resistance: High blood sugar levels, fatigue, increased appetite, weight gain and brain fog.

  • Symptoms of Hormonal Imbalances: Present itself in the form of hypothyroidism, hyperthyroidism, PCOS, estrogen-dominance, and more.

Diagnosis and Treatment

Again, working with a practitioner will be your best bet. If you are presenting other symptoms in addition to IBS, you can do different blood and hormonal panels to properly diagnose and treat. I believe working with a naturopathic or functional medicine doctor will give you the full picture when it comes to treatment.

Some basic treatments for helping to support your body's metabolic function are:

Blood Sugar Management

Avoid constant spikes and crashes in your blood sugar levels, leading to insulin resistance over time. Adding healthy fats and proteins to each meal can reduce high spikes in blood sugar. Incorporating bitter foods before your meal (greens, then protein, then carbs) can help reduce the overall spike of your blood sugar when eating. Eating three meals a day and avoid constant snacking allows your body time to properly digest food. Lastly, eating at least 2-3 hours before bed to help support your body’s digestion.


Root Cause #5: Peristalsis

The final root cause we will review is a lesser talked about one for constipation. Peristalsis, the rhythmic contraction of muscles in our GI tract, is crucial for digestion. It helps push food through your digestive system, starting in your throat and down to your colon. However, this automatic process can be disrupted by the nervous system’s response to stress.

The vagus nerve, a major component of the central nervous system, serves as a vital link between our brain and digestive system, coordinating peristalsis. In times of stress, the vagus nerve can be triggered, pushing us into a fight/flight mode.

When our body perceives danger, whether from external stressors like work or internal factors like trauma, it triggers the nervous system's fight or flight response, impacting peristalsis.

While we no longer have the same type of impeding danger like our ancestors (idk about you but I don’t have to watch out for a tiger about to eat me) chronic stress can disrupt the intricate interplay between the nervous system and our digestive system. This can lead to increased peristalsis, causing diarrhea, or decreased peristalsis, resulting in constipation.

Further motility issues and digestive disorders could arise, potentially leading to complications such as chronic constipation and bacterial overgrowth because we are not able to regularly clear out waste. Basically, stool is just sitting in your colon and toxins and bacteria can build up.


But don’t lose hope! There is a way to help overcome hyper/hypomotility within your gut and regulate your nervous system.

Regulating Peristalsis

One of the ways to help regulate peristalsis is through regulating your nervous system. You need to activate the vagus nerve, so your body shifts to a rest and digest, or parasympathetic state.

You can activate your vagus nerve via meditation, belly breathing, humming, or even putting your feet up on a wall! You can also incorporate acupuncture and chiropractic care. I loved getting weekly acupuncture and found it really beneficial in combating chronic stress.

Lastly, mindful eating could be really beneficial. Sometimes, it’s not what we eat, but how we eat it. Slowing down our mealtime, practicing gratitude, and eating without distraction can help with motility issues.


Don't take laxatives as your final answer to treating chronic constipation. There are a multitude of reasons why you may be experiencing chronic constipation. Working with a practitioner to finding your root cause can make a huge difference. It's time to treat the root issue and not just put a Band-Aid on your symptoms!

And remember, healing is not a linear journey! So, even if you do continue to experience constipation from time to time on your gut healing journey (as I know I do!), it’s important to communicate this with your practitioner. You are not alone! Healing takes time 🤍



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Welcome! If you made it here, you are probably looking for answers on where to begin your wellness journey. I'm Jessica, and I started my gut health journey over 3 years ago. As an avid foodie and wellness enthusiast, I hope to inspire you on your realistic wellness journey.

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