Digestion 101: Process and Issues

Adapted from episode 68 of The Perfect Stool podcast and edited for readability.

I’m going to describe the digestive process when it’s working well, which may help you pinpoint where things may be going wrong for you, as well as give you an idea of the symptoms when a certain part of your digestion is off. I’ll be focusing mostly on functional digestive issues, as those are the kind I work with clients on, as opposed to mechanical issues, which a conventional gastroenterologist is best equipped to handle, although I’ll mention a few. And I’ll preface this by saying that of course this isn’t comprehensive, but rather a summary of some of the most common issues I see in clients. 

So first of all, before you even eat, as you think about eating or smell your food before eating it or while cooking it, this alerts your brain to start the flow of saliva in your mouth, which contains salivary amylase, which helps break down starches in your food into simpler sugars. Then next, if you don’t shovel your food down too quickly, you’ll ideally chew each bite a good 20 or 25 times so that it’s a fine mush and it mixes well with those enzymes. 

Then as you swallow, your food travels down the esophagus to your lower esophageal sphincter, which will open up and let the food into your stomach. Now hopefully the pH in your stomach is ideal, meaning not too acidic and not too alkaline, although a stomach with its acid is quite acidic, with a pH usually in the range of 1.5 to 3.5.  

When it’s not acidic enough, or there’s a lack of stomach acid, called hypochlorhydria, it can lead to the opening of the lower esophageal sphincter, which is sensitive to pH and closes when the pH drops under 3.0, which will trigger the escape of stomach acid into the esophagus and the sensations of GERD, or gastroesophageal reflux disease, aka heartburn.  Stomach acid tends to decrease with age but can also decrease due to the presence of H pylori or Helicobacter pylori, the bacteria that causes ulcers and stomach cancer when it possesses certain virulence factors. Other factors impacting stomach acid are alcohol use, poor diet, not being in a proper rest and digest or parasympathetic state while eating, stress and food sensitivities as well as pharmaceuticals such as antibiotics, proton pump inhibitors or PPIs and antacids. Insufficient stomach acid can lead to maldigestion of proteins and their components, amino acids, which can impact the lining of the stomach leading to leaky gut, and puts stress on the pancreas to produce enzymes to complete the digestive process (which are composed of amino acids themselves). And when you have undigested proteins leaking into the abdominal cavity, that can trigger autoimmune reactions as your immune system targets the proteins and other parts of your body that look similar to the offending proteins. Low stomach acid can also lead to overgrowths of candida, parasites, and bacteria, which are normally killed off or kept in check by stomach acid, and can also lead to mineral depletions in the body. 

Another possible reason for GERD, proposed by Norm Robillard who appeared on episode 41 of this podcast and created the Fast Tract Diet and wrote Heartburn – Fast Tract Digestion: Acid Reflux & GERD Diet Cure Without Drugs*, is an overgrowth of bacteria in the small intestine feeding on maldigested carbohydrates, which leads to the production of gas. That gas puts upward pressure on the stomach and causes acid to be pushed back upwards. This maldigestion can be the result of excess starches in the diet and/or excess bacteria, as well as insufficient pancreatic enzymes to help digest the starches. Upward pressure can also happen as a result of a hiatal hernia.

But back to your stomach, when the food arrives there, your stomach’s G cells release a hormone called gastrin, which triggers the stomach to release gastric juice, composed of water, mucus, hydrochloric acid, pepsin and intrinsic factor. The churning motion of your stomach helps to mix up the food with gastric juice and break it down. And then the pepsin, in combination with the acidic pH produced by the hydrochloric acid, breaks down proteins into amino acids. 

There are a few things that can go wrong at the level of stomach that can cause problems. Gastritis, or inflammation of the lining of the stomach, can come about due to a poor diet, excess alcohol consumption, overuse of NSAIDs or non-steroidal anti-inflammatory drugs, especially ibuprofen and naproxen sodium, and H pylori overgrowth, which can be the result of lowered gut immunity due to stress. While virulent strains of H pylori can causes ulcers and stomach cancer, even non-virulent strains can still cause GERD and bloating after eating, stomach pain, especially on an empty stomach, nausea, and other symptoms like lack of focus, especially in children, constipation, diarrhea and even insomnia. 

And while actual tests of people with symptoms of GERD have shown that hypochlorhydria is the most common cause (roughly 80% of the time), you may actually have excess stomach acid or hyperchlorhydria, which is commonly treated with PPIs by conventional doctors, whether or not the state of your stomach acid is known (which is rarely as few doctors have the ability to perform a Heidelberg test, which measures stomach acid). Hyperchlorhydria is also common in the early stages of an H pylori infection but usually turns into hypochlorhydria over time. But it’s important, even if you do have excess stomach acid, to not stay on PPIs long term. Usually a course of 2 weeks is recommended and then other causes of your issues should be investigated. 

So after the stomach, the food goes through the pylorus into the small intestine or small bowel where it’s broken down further with enzymes produced by the pancreas, the primary types being amylase for breaking down starches, proteases (also called proteolytic enzymes, proteinases or peptidases) for breaking down proteins and lipase for breaking down fats, along with bile. Bile is produced by the liver and stored in the gallbladder and it emulsifies fat, meaning it breaks it down into micro-droplets. Also involved in the final stages of digestion of carbohydrates and protein are the brush border enzymes, which are embedded in the microvilli, or hairlike structures lining the small intestine, the most well-known of which is lactase, which breaks down lactose, the sugar in dairy products. Genetics determine the persistence of lactase activity, which many people lose by adulthood, making them lactose intolerant, whose symptoms are gas, painful, soft or even liquid stool, bloating, cramping and discomfort after eating and while eliminating lactose, which is highest in soft cheeses, milk and ice cream. 

Issues at this level can be related to insufficient pancreatic enzymes, which can have many causes. The official name of this is called exocrine pancreatic insufficiency or EPI, whose most common cause is chronic pancreatitis or inflammation of the pancreas. This can result from alcohol abuse or gallstones in the gallbladder. Ongoing inflammation damages the cells of the pancreas, leading to a decrease in enzyme production. Other causes of EPI include celiac disease, IBD, diabetes, pancreatic cancer and weight loss or other digestive tract surgery. Symptoms of EPI are either constipation or diarrhea, abdominal pain, bloating and gas and fatty or pale-colored, oily or floating, smelly stools. 

And returning to the gallbladder, you can also have issues impacting your digestion originating in the gallbladder such as gallstones, clogged bile ducts, sludgy bile or insufficient bile, which is a given if you’ve had your gallbladder removed. Although the liver produces bile, it’s stored in the gallbladder and you won’t have enough to digest a higher fat meal. Signs of insufficient bile or fat maldigestion include trapped and bad-smelling gas, stomach cramps, diarrhea, erratic bowel movements, weight loss and pale-colored stools. Having problems with fat digestion or having had your gallbladder removed leads a lot of people to avoid eating fat, which is a mistake, because it’s part of a healthy diet and is necessary for the absorption of your fat soluble vitamins A, D, E and K as well as fat soluble vitamin-like compounds like CoQ10. If you’ve had your gallbladder removed, you should continue to eat fat but support your gallbladder with something like Bile Acid Factors*. If your bile is insufficient for other reasons, you may need to stimulate bile production with bitter greens, green leafy vegetables, beets, artichokes, pickles, grapefruit, lemons, limes and their juices and zest, spices such as fenugreek seeds, cinnamon stick, turmeric and ginger or drinks like roasted dandelion root tea, lemon tea, celery juice and coffee.

There are also lots of things that can go wrong at the level of the small intestine that can impact digestion. From the bacterial perspective, there’s SIBO, or small intestine bacterial overgrowth, which is usually caused by stagnation in the small intestine due to a variety of causes. That stagnation leads to a buildup of excess bacteria and general dysbiosis, or an overgrowth of the wrong types of bacteria. This can cause painful bloating and distention of the abdomen after eating, and if the bacteria produce hydrogen, usually diarrhea or soft stool. If your overgrowth is of hydrogen sulfide producing bacteria, then you’ll likely also have gas that smells like sulfur or rotten eggs and excessive belching. Other possible signs of hydrogen sulfide SIBO include intolerance to sulfur-containing foods and supplements, weight loss, brain fog, exercise or stress intolerance, burning bladder syndrome, elevated heart rate, insomnia and low blood pressure after eating. Hydrogen sulfide SIBO is also associated with ulcerative colitis, Crohn’s disease and colorectal cancer. 

Then there’s IMO, or intestinal methanogen overgrowth, which used to be known as SIBO-C, or SIBO with constipation, which is an overgrowth of archaea (which are like bacteria but of a whole different domain) including Methonobrevibacter smithii and Methanosphaera stadtmanae, which produce methane gas by metabolizing the hydrogen produced by bacteria fermenting carbohydrates. You’ll often have bloating and gas with a metallic smell when this happens. 

Or you can have an overgrowth of candida, which is a normal resident of your gut but can overgrow and even become systemic in severe cases, and which can form hyphae or sort of tails that go out between cells lining the small intestine. Usually bloating after eating, food sensitivities, skin issues and brain fog are signs of invasive candidiasis. 

Any of the above small intestine issues can lead to a case of intestinal permeability or leaky gut, which means that bits of not quite digested food or bacterial body parts called lipopolysaccharides or LPS can escape either through broken down cells or between cells and get into your system, activating your immune system and often leading to autoimmune diseases. 

But back to the normal digestive process, after the small intestine, food moves through the ileocecal valve to enter into the large intestine. Some people have mechanical issues with this valve staying chronically open or closed. Chronic constipation and tenderness in the lower right quadrant are signs that this may be an issue and it can be a root cause of SIBO. You can actually manually reset this value and I’ll link to a video about how to do that. 

And I should also mention the role of the vagus nerve in all this, because the vagal nerves carry signals between your brain and digestive system. And damage to the vagus nerve from a traumatic brain injury, diabetes, stomach surgery or certain medications, or dysfunction from emotional trauma and stress can impact your digestion, causing problems like gastroparesis, or food not moving from your stomach into your intestines properly, or SIBO. One simple way to check your vagus nerve function, described in the book Accessing the Healing Power of the Vagus Nerve* by Stanley Rosenberg, is to look at your uvula (the thing that hangs down in the back of your throat) in the mirror while saying “ah, ah, ah” and if it pulls up to the right or left, you may have issues. If this is the case, there are exercises listed in that book that can help you return to normal vagal tone. 

And of course you can have autoimmune issues all the way along, starting in the stomach, where pernicious anemia is an autoimmune attack on the parietal cells lining the stomach that produce stomach acid and intrinsic factor, which allows you to absorb vitamin B12. Or you can have post-infectious IBS or irritable bowel syndrome, which is an autoimmune attack on a protein called vinculin, which helps the migrating motor complex function to remove food from your small intestine on a regular basis. Or you can have celiac disease, which is an autoimmune attack on the microvilli lining the small intestine when you eat gluten. Common signs of this are stomach pain, fatigue due to malabsorption of nutrients as the microvilli deteriorate and diarrhea. You can also have other food sensitivities and intolerances such as non-celiac gluten sensitivity or lactose intolerance, which are two of the most common. 

Or you can have inflammatory bowel disease, which is an autoimmune disease that can manifest as ulcerative colitis or Crohn’s disease. Crohn’s involves plaques of diseased, ulcerated tissue anywhere from your mouth to your anus, and in its most severe form can lead to twists and strictures in the intestines, openings or fistula in the perianal area, anemia, shortness of breath and inflammation in your skin or joints. Common earlier signs of Crohn’s are pain, abdominal cramping, diarrhea, fatigue, fever, blood in the stool, loss of appetite, weight loss, food sensitivities, a sense of incomplete elimination after a bowel movement and bowel urgency. Colitis takes many forms such as pancolitis, microscopic colitis, ulcerative proctitis, etc. depending on its location and form, but always involves inflammation and ulcers in some part of the colon. Signs of colitis include abdominal pain, diarrhea, bowel urgency, blood and/or pus in the stool, weight loss, rectal pain, nausea, vomiting, loss of appetite, chills or fever and anemia. 

So back to normal digestion, when the food reaches your large intestine, normally you’ll be absorbing water, minerals and some remaining nutrients from your food. And if you have a healthy, fiber-rich diet, you’ll also have lots of fiber left over for the bacteria, which are most abundant in your large intestine, to ferment. The bacteria will also be providing nutrients themselves, specifically B vitamins and vitamin K, from that fermentation process. And they will also be extracting the short chain fatty acids butyrate, propionate, and acetate from the fermentation process.

Butyrate has been the target of a lot of research recently and I’m sure you’ve heard me mention it, as it produces 70% of the energy for the cells lining the large intestine or the colonocytes and helps maintain a hypoxic or oxygen-free atmosphere in the colon. The colonocytes break down butyrate and the other short chain fatty acids through a process called beta oxidation, which requires large amounts of oxygen. When there’s a lack of fiber for producing butyrate or following antibiotic use, you can have a breakdown of this process, leading to a loss of gut barrier function, and a subsequent increase in oxygen in the colon. That increase favors the expansion of proteobacteria, a phylum of bacteria that contains many gut pathogens like E Coli, Pseudomonas and Campylobacter, which are facultative anaerobes, meaning they can live in the presence of oxygen. This helps them outcompete the beneficial obligate anaerobes, particularly Clostridia, which are butyrate producers. I’ll link to a Lucy Mailing article explaining all about this particular type of dysbiosis. But what I’ve found with clients is that if you tend to have loose, messy stool, it’s often the result of this kind of dysbiosis, and supplemental butyrate in the form of Probutyrate (find in my Fullscript Dispensary*) or Tributyrin* is helpful in breaking this cycle. 

And I should probably mention constipation at this point because that’s something else that can go wrong. Having fewer than one bowel movement a day or having stool that’s very dry and hard or even to the point of rabbit pellets, hard to pass or feeling incomplete is considered constipation. You may also see breakthrough diarrhea as well in the context of constipation or what’s considered IBS-M or mixed.  Constipation can be the result of dehydration, lack of exercise, a low-fiber diet, changes to your routine, an intolerance to or large amount of dairy products, stress, chronic holding of bowel movements and certain medications. This can lead to anal fissures, diverticulitis or infected pouches in the wall of the large intestine, or hemorrhoids, which can all cause pain in the colon. And anal fissures and hemorrhoids can cause bleeding, which will show up as bright red on the toilet paper. 

But if everything is going well and properly with your digestion, you’ll instead have 1-3 regular bowel movements a day, around a 3 or 4 on the Bristol stool chart, that pass easily and completely and result in a clean wipe of the toilet paper most of the time. 

If your digestion is not proceeded successfully as describe above and you’re suffering with any type of gut or digestive issue, you’re welcome to set up a free, 30-minute breakthrough session with me (Lindsey). We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

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