Mechanisms behind bowel dysfunction

Dr. Laura Roxann Alexander
15 min readApr 17, 2024


Most adults don’t talk about their bowel movements. However, optimal bowel movement is a key marker for health and one that some doctors may ignore. Constipation or diarrhea can lead to chronic disease and become a gateway for a simmering infection that might last years. There are many common mechanisms that can cause bowel dysfunction and the health of your microbiome can even be a root cause of acid reflux or irritable bowel syndrome. The digestive process is often a bit mysterious, we can’t see it, but we know it happens at least 3 times a day. In this article I want to explain the key components of the digestive process, what each organ does, and how there can be dysfunction at every step.

The Nervous System

So let’s start at the top and work our way down. You may think the stomach is the beginning of the story, however, it is the brain and parasympathetic nervous system that begins the digestive process. Digestion starts with our ability to be in a rested state. Specifically, the parasympathetic nervous system rather than the sympathetic nervous system. These two arms of the nervous system coordinate in any given moment to keep us alive and we must be able to move between the two arms easily. The sympathetic nervous system gears us up for fighting or fleeing for safety. The parasympathetic nervous system signals the organs and glands that all is well and to rest, digest our food, and clean house.

The body must be in a parasympathetic state to support all digestive processes. There is no question that stress (real or imagined) impacts our bodies ability to digest food, absorb nutrients, and excrete waste. The vagus nerve is the main driver of parasympathetic regulation. It is called the vagus meaning “wandering” because it starts at the brain stem and wanders all the way to the groin. It innervates every major organ that is associated with digestion, including the pancreas, liver, and gallbladder. Signals from the brain and vagus nerve to the gut initiate important action steps in the digestive process.

  1. Stimulates release of stomach acid from the parietal cells in the lining of the stomach and the physical churning of the stomach and it’s contents.
  2. Stimulates the migrating motor complex, a bundle of nerve fibers surround the intestines that produce wavelike contractions that move food along the intestinal track.
  3. Stimulates the pancreas to release digestive enzymes

Signaling to the gut is of the highest importance to our well-being. In fact, low vagal tone has been linked to many chronic conditions like irritable bowel disease, cardiovascular disease, and mood disorders.

If we are eating in a rushed or stressed state, vagal stimulation will be suppressed and these critical digestive functions will not happen! Stress stops digestion-why? Because why would you need to spend energy digesting your food if survival is not assured?

The Mouth

Next stop in the digestive process is the mouth. This stage of digestion is fully within our control and what we do here can make a huge difference in terms of healing and symptom control. The concept of eating hygiene should be applied to every single meal, it’s that important. Eating hygiene is a set of principles that you can apply each time you sit down to a meal. I have seen many clients improve drastically, just by applying these simple concepts.

  1. Chew your food! Ideally until it is mush. Antihistamines can impair this phase of digestion by reducing saliva. Saliva has enzymes within it that start to break down complex carbohydrates. The longer you chew your food, the sweeter it may taste!
  2. Do not drink copious amounts of liquid during meals. Liquid dilutes stomach acid and all digestive enzymes which lead to indigestion.
  3. Take at least 20 minutes to eat. It takes that long for satiety hormones to tell the brain you are full and to stop eating. Eating fast delays this release and can lead to over-eating.
  4. Be present. Turn off electronics. Sit with yourself and notice how you feel. Notice the food and what it tastes and feels like as you eat it.
  5. Breathe between bites. Put the fork down. Maybe even do 3 rounds of box breathing before you begin your meal.
  6. Create an environment of safety so the vagus nerve will stimulate the digestive process.
  7. Do not eat on the run. It would be better to skip the meal and wait until you are in a parasympathetic state.
  8. Meals are acts of self-care. Treat them as such.
  9. Snacking can disrupt the digestive process. Do not snack (more on this later) if you are trying to heal the gut.

The Stomach

So many processes can go wrong in the stomach and there are many myths that continue to lead people to pop acid reducers as if their lives depended on it. Yet the majority of the cases of acid reflux is not about too much acid, but stress combined with minimal chewing that puts too much pressure on the stomach to blend the food.

I suffered with acid reflux for 20 years, saw a handful of gastroenterologists, and took over 4 different acid reducers (all of which eventually stopped working). It really wasn’t until I got so frustrated with doctors telling me I just had too much stomach acid and that the only solution was to take an acid reducer twice a day, that I began to look for the real reason why I had heartburn. Surprise, it wasn’t because I had too much stomach acid. In fact, that is a very rare condition. They can measure the pH of stomach acid now with a tiny capsule that can swallowed and then pooped out after 24 hours. I haven’t yet met someone whom this expensive test would be warranted. Instead there are many common reasons why a person may not have enough stomach acid or have stomach acid in the wrong place, which is what causes heartburn and GERD symptoms.

I cured my acid reflux by eliminating foods that I reacted too, which included beef, dairy, and bananas, as well as a list of 10 or 12 other foods. I stopped eating processed foods and getting take out from restaurants. I also began to practice eating hygiene techniques and I ate slower and chewed more. If you want to find out more about the side effects of acid reducers and long term consequences of their use, follow the link below.

Acid reflux is rarely caused by too much acid. Hydrochloric acid is vital to digestion and when we increase the pH of the stomach to a more basic or alkaline pH, digestion is impaired. We must digest our food to be able to absorb nutrients. Stomach acid is also the first line of defense against pathogens coming in on our food. When the pH is more basic, pathogens have a higher chance of making it into our small intestine where they can set up shop.

The Magic of the Small Intestine

The real magic happens in the small intestine where the bulk of nutrient absorption occurs. It really is like magic when all systems are go, but when there is dysfunction anywhere in this process you may get nutritional deficiencies but also inflammation that can move outside the intestinal track and into the systemic circulation and therefore other tissues and organs.

The top 8 reasons why we may have dysfunction in the small intestines

  1. Transit time and motility dysfunction. You want your bowels to move; not too fast or not too slow, but just the right amount of time to move food and absorb nutrients.
  2. Stress decreases all digestive secretions on purpose!
  3. What didn’t happened upstream from the small intestine like in the stomach or mouth?
  4. Damage to the gallbladder and pancreas as well as insulin resistance which impacts energy generation. All organs, cells, and tissues need energy to work. The gallbladder releases concentrated bile to digest fats and acts as an antimicrobial. Liver and gallbladder health impact digestion and if the gallbladder is removed then fats cannot be absorbed as readily.
  5. Microbes also impact digestion. This dynamic can be incredibly complex.
  6. Genetics may play possible role in digestive capacity and ability to make enzymes which degrade histamine which can lead to diarrhea and histamine overload.
  7. Leaky gut and immune system dysregulation- Food sensitivities don’t just randomly develop. Our intestinal wall must be optimally permeable. We want nutrients to pass through but we don’t want microbes and undigested food particles to pass through the wall and be seen by our immune cells. Two-thirds of the immune system reside in the gut and leaky gut can not only cause damage in the intestinal track, but lead to chronic systemic disease as well.
  8. Medications and alcohol can damage the protective mucous layer and the intestinal cells themselves. Ibuprofen and aspirin degrade the mucous barrier which allows microbes to move closer to the intestinal wall and our immune system. Estrogen can cause the bile to thicken which will clog up the gallbladder ducts and liver. Oral birth control has been linked to gallstones and gallbladder damage which may result in removal.

Diarrhea causes deficiencies

Optimal bowel movements are one formed per day with minimal gas or odor. Loose, pencil-thin, watery, or mush are signs of a rushed bowel movement. Diarrhea can also cause dehydration as well as insufficient absorption of fats, minerals, and fat soluble vitamins because those take longer to absorb.

Food can be a huge driver behind diarrhea, especially under-diagnosed lactose intolerance and fat malabsorption. Food sensitivities and allergies can cause diarrhea as well and many people try food elimination diets without success because they do not remove the culprit for a long enough time period. If the allergy is mediated by IgG antibodies, it can take 21 days for those antibodies to leave circulation. Specific food eliminations should be at least 4 months long.

Sugar alcohol sweeteners or too much fructose can also cause loose or watery stools. Even in the short-term, diarrhea caused by this dynamic can cause deficiencies and impact our overall well-being.

Genetics may play a significant role in diarrhea if food eliminations and other drivers have been explored with limited success. People can have genetic variants in the enzymes necessary for histamine degradation as well as enzymes that breakdown fructose. I recently did a genetic test and found out I had two variants on both enzymes needed for histamine degradation. This connection was huge for me, since I seemed to have a stuffy nose and watery eyes most days regardless of the weather outside. Following a low histamine diet and the addition of supplements which help breakdown histamine has improved my symptoms.

Other drivers behind diarrhea include medications, lack of fiber, stress, alcohol use, and our microbiome.

Constipation- How often do you go?

Normal bowel movements happen daily, not every 2 to 3 days. We must move waste, undigested fivers, dead bacteria, live bacteria, toxins, and even compounds our body makes like estrogen and cortisol, out of the body daily. Stool is the primary pathway for elimination. If we don’t eliminate it, then everything listed above has the opportunity to be reabsorbed back into the blood through the colon. Waste is toxic, the longer it sits in the colon the more likely it can cause damage to the coloncytes though inflammation.

Common causes of constipation:

hypothyroid disease


insufficient magnesium


insufficient fiber

These root causes are much harder to discover and often coincide with each other or another disease state.

Food sensitivities

Insufficient fat

Microbial imbalance

Insufficient serotonin action

Insulin resistance

Excess Vitamin D which depletes magnesium

Dysbiosis: Too much and in the wrong place

Our microbiome can be behind diarrhea and constipation and often leads to a large amount of suffering, misdiagnosis, and multiple chronic diseases.

Dysbiosis is a microbial imbalance and can be caused by many different factors.

  1. An overt infection with a pathogenic species
  2. An opportunistic overgrowth of a species that may create compounds and gases that lead to low-grade inflammation
  3. Not enough diversity within the microbiome like in the case of someone who has taken multiple rounds of broad spectrum antibiotics througout their life
  4. Not enough beneficial bacteria
  5. Bacteria in the wrong place that have migrated up from the large intestine into the small intestine.

One of my favorite analogies to use is a playground. Picture lots of kids, teachers, and even some bullies, all interacting on a playground. What would happen if the teachers leave or if there are too many bullies? You might get some pushing and shoving and probably even some scrapped knees and tears. We can picture that happening in the small intestine. Some bullies (pathogenic species) can produce specific gasoues byproducts like methane and hydrogen sulfide which can cause diarrhea, constiptation, bloating, and pain. When that happens, you might be labedled as having Irritable Bowel Syndrome. However, that is not the full picture and often leads people to prescription medications which decrease or increase the transit time of waste, totally missing the the root cause of disease.

Irritable Bowel Syndrome or Small Intestinal Bacterial Overgrowth

IBS is a label. The real question is why do you have it? If you go to a traditional medical doctor with a mix of constipation, gas, bloating, diarrhea, or abdominal pain they will give it a name. You may be prescribed a medication for motility which will slow the diarrhea or increase your bowel movements. I’ve had some clients be told it was nerves or hormones and they didn’t get much help at all, especially if they have what is considered mild symptoms. None of those strategies help in the long run because the real reason behind the gut dysfunction is still happening.

Root causes of irritable bowel:

  1. Maldigestion from insulin resistance, hypothyroid, stress, and poor eating hygiene.
  2. Dysbiosis or variations of bacterial or fungal overgrowths in the small intestine. These bacteria make gas as a natural byproduct of metabolism and the gases-either methane, hydrogen sulfide, or hydrogen- can cause diarrhea or constipation.
  3. Gallbladder and liver dysfunction from thick bile which may lead to fat maldigestion and malabsorption.
  4. Digestive intolerances like lacking the enzymes to digest fructose or lactose and/or food sensitivities that may create inflammation which further damages the lining of the small intestines.
  5. Medications like acid reducers, serotonin reuptake inhibitors and birth control can damage the small intestine in a myriad of ways. Reducing acid production and increasing the pH reduces our first line of defense from pathogens coming into the body through food. One bacteria in particular, Helicobacter Pylori, thrives in a basic environment and is primarily found in the stomach.

Each cavity of the gastrointestinal track is separated by sphincters and the natural process of cleansing waves (think little brooms sweeping the waste and food debris downstream) keeps bacteria from migrating up into areas where they can set up shop and overgrow. However, if someone is suffering from many of the above dynamics, they are at risk of having a overgrowth, SIBO for short. An overgrowth can occur with many different species of bacteria but also yeast and fungal species can be present as well. Often people need an herbal or prescription antimicrobial to reduce the overgrowth and at the same time probiotics may be used. Stress and digestive sufficiencies must be addressed or SIBO can come back. In fact stress plays a big part in this entire process. The ability of the body to rest and digest will support the natural cleaning of the intestines.

If someone is on medications for motility but not addressing any other factors, they are likely to get some relief but overtime their symptoms may get worse. The inflammation occurring from an overgrowth can lead to further damage in the gut and risk of systemic diseases like autoimmune diseases, cardiovascular diseases, and cancer.

The Poop Percolator

The colon is home to trillions of organisms. It even contains a cluster of bacteria known as the estrobolome. Bacteria in this category produce an enzymes called beta-glucuronidase, which can cleave estrogen from it’s carrier, allowing estrogen to be reabsorbed back into systemic circulation. This dynamic may actually be a root cause for women with estrogen dominant symptoms and constipation. The longer the stool sits in teh colon the more likely estrogen could be reabsorbed.

Low fiber diets create inflammation here because these bacteria thrive on both soluble and insoluble fiber. Most food has been absorbed in the small intestine and only fiber makes it way to these organisms. There are several species of beneficial bacteria that use these fibers to produce short chain fatty acids that the body and our coloncytes use for fuel.

The colon is affected by everything that does or doesn’t happen upstream from it. Colonoscopy screening is early detection but it is not prevention. I believe an alternative to a colonscopy screening should be a patient history form that would include questions like how often do you have a bowel movement or describe your bowel movements. Colon cancer risks are factors that could be addressed years before cancerous polyps form. Those risks include diarrhea, irritable bowel syndrome or inflammatory bowel disease (IBD), diets high in processed meats like pork, bacon, hot dogs, and red meat, diets low in plant fibers, and the standard american diet. To my knowledge, most traditional medical doctor history forms just ask if you have been diagnosed with IBS or IBD but they don’t ask detailed questions. We are missing these dynamics for years!

Waste must be moved out. Waste includes bacterial body parts, food debris, hormones and endogenous compounds made by the body, and toxins. None of those things we want back into the body. Constipation should not be overlooked or downplayed. It can have serious consequences.

Strategies to improve gut function

So what are long term strategies to keep your gastrointestinal system healthy and reduce the risk of inflammatory bowel conditions, cancer, and nutrient malabsorption?

  1. You are unique. Your biology is unlike any of person on the planet. Your environment impact your biology. Your microbiome is unique, therefore you must eat food that serves you. You must pay attention to the signs and use the symptoms your body is giving you as a wake-up call. It takes energy to give you signs, pay attention!
  2. Eat food that your great grandparents would recognize as food. Don’t eat food that you would have to eat if there was a zombie apocalypse.
  3. There are so many great books written to help people find eating strategies that will work for them as well as cure and reverse gut disorders. Seek those out. They will give you more information than a 10 minute doctor appointment.
  4. There are so many “diets” out there that it can be confusing. The gold standard diet for those with gut dysfunction is some type of elimination diet. Begin with eliminating processed foods and eating a clean, Paleo or Mediterrian inspired diet. Both of those are backed by research. It may take a more intense elimination so I do encourage people to work with a practitioner or specializes in gut disorders. This would not be a typically GI specialist in the medical field but someone who uses diet and food as medicine.
  5. Meal timing is incredibly important for those with gut issues. A minimum of 12 hours of an overnight fast will allow the cleansing waves to occur and sweeping of debris downstream. A 4 to 5 hour window between each meal also allows the gut to rest and clean. Do not snack! That can be a root cause of gut dysfunction as well as blood sugar dysregulation.
  6. Read the food label. Know exactly what you are eating. There are many additives in processed foods that are harmful to our gut microbiome and our intestinal cells as well. Preservatives are especially harmful. Organic doesn’t mean healthy. Organic chips are still chips! Try to purchase foods with minimal ingredients and be sure you know what those are.
  7. Reduces stress. Find a book to help you incorporate stress reducing techniques into your everyday life. Try meditation and mindfulness eating. Find a way to live in a rested state most of the day.
  8. Exercise is a must. Movement in different planes of direction at different rates. Resistance training and yoga are the top two forms of exercise I recommend. Both have a mindfulness component to them as well as different plans of motion.

Gut healing takes time. We eat 3 times a day and that is a 3 opportunities to bring in food that can help you heal or food that create more damage. It may take multiple versions of your plan to find what works for you. It may involve antibiotics or antimicrobials to eliminate an overgrowth.

Don’t forget that the top of the GI tract is our brain. Our thoughts and the perceived stress that occurs directly impacts the entire digestive process. Restoring the health of the gut must include mindfulness techniques or gut dysfunction will most likely come back.



Dr. Laura Roxann Alexander

Pharmacist.Personal Trainer.Lift heavy, skip the run.Let food by thy medicine and medicine be thy food.