In part 2 of this series on digestion, we dive into pathology of the stomach, small intestine, and the digestive juices secreted into the small intestine by the pancreas, gallbladder, and liver. Diet, lifestyle, and supplementation to support these pathologies are discussed as well.

In this post, we are continuing our digestion discussion with pathophysiology in the stomach and small intestine. As a refresher from last post, remember that the stomach and small intestine are where the bulk of digestion and absorption take place. The stomach is where the process of protein digestion begins with the help of hydrochloric acid and pepsin. The small intestine is where digestive secretions are deposited by the pancreas, liver, and gallbladder to break down fats, proteins, and carbohydrates as well as where most absorption of nutrients occurs. 

Picking up where we left off last post, the next possible problem with digestion is inadequate stomach acid production or hypochlorhydria. As discussed in the previous post, stomach acid is needed for activation of pepsin and for proper digestion, mainly of proteins. The use of antacids to lower stomach acid production is a common remedy used by people with digestive issues, particularly Gastroesophageal Reflux Disease (GERD), because many people believe that too much stomach acid is their problem although most of the time, the problem is actually due to deficient stomach acid. One of the common types of antacids used are proton pump inhibitors (PPIs) These drugs are associated with increased risk of osteoporosis, heart arrhythmias, intestinal infections, bacterial pneumonia, and multiple nutrient deficiencies because stomach acid is needed for the proper release of nutrients from foods. Particularly, low levels of vitamin B12, magnesium, and iron are low in people with long term use of PPIs. 

Let’s break down the feeling of GERD that most people associate with too much gastric acidity. In GERD, the burning feeling is due to stomach acid burning the esophagus. The esophageal sphincter is what separates the esophagus from the stomach and keeps stomach acid from burning the esophagus. That sphincter is controlled by pH. So, if the pH is low due to sufficient hydrochloric acid (remember low pH is associated with acids on the pH scale), the sphincter will clench tighter to prevent content backflow. However, if the pH is high due to lack of acidity, the sphincter will not clench as tightly, so there is a higher change of hydrochloric acid coming up into the esophagus causing GERD. 

Common signs and symptoms of low gastric acidity include bloating, belching, burning sensation, and flatulence immediately after meals, sense of excessive fullness after eating, indigestion, diarrhea, constipation, multiple food allergies, and weak, peeling, and cracked fingernails. Diseases that are associated with low gastric acidity include Asthma, Autoimmune disorders, Celiac disease, Diabetes, Eczema, Graves’ disease, Osteoporosis, Pernicious anemia, Rheumatoid arthritis, and Rosacea.

If you have hypochlorhydria, it is important to address the underlying cause of low stomach acid. Some of the major underlying causes of hypochlorhydria include gastritis, Helicobacter pylori (H. pylori) overgrowth, and taking acid reducing medications. Some other factors that may lead to low stomach acid include eating too quickly, high sugar intake, zinc deficiency, age, and food sensitivities. H. Pylori overgrowth can be caused by low hydrochloric acid or result in low hydrochloric acid. Hypochlorhydria can cause H. Pylori overgrowth because the higher pH provides a favorable environment for colonization of organisms such as H. Pylori. H. Pylori overgrowth can also cause hypochlorhydria because it damages the lining of the stomach, which impairs the cells that produce hydrochloric acid and reduces hydrochloric acid production.

Supplements that may support the body fighting H.Pylori include Deglycyrrhizinated Licorice (DGL), Garlic, and Biocidin. DGL helps promote healing of ulcers caused by H. Pylori, stimulates mechanisms that prevent ulcer formation, and may inhibit the growth of H. Pylori. The DGL supplements we recommend are Rhizinate DGL Integrative Therapeutics and DGL Ortho Molecular. Garlic has shown to be effective against the bacterial strain H. Pylori so it can be helpful for killing off the overgrowth in the stomach. The aged garlic supplements we recommend include High Allicin Garlic Arcana (Allicin is the active compound in garlic with the anti-microbial benefits), Kyolic Garlic Original Formula, and Kyolic Reserve. Biocidin helps break through the heavy duty biofilms of H. Pylori that it used to protect itself; it also contains anti microbial herbs that together may support the removal of H.Pylori. The different forms of Biocidin are Biocidin capsules, Biocidin liquid, and Biocidin LSF.

After addressing underlying causes or while supporting your body with diseases that lead to hypochlorhydria, you can focus on diet, lifestyle, and supplementation to support hydrochloric acid production. Dietary changes that can support stomach acid production include lowering sugar and processed food intake, making sure to get enough zinc in the diet, and using apple cider vinegar.

Sugar and processed foods can cause inflammation in the stomach, which can decrease acid activity since the cells that produce stomach acid are part of the stomach wall. This is why decreasing these foods may help improve stomach acid production. Additionally a zinc deficiency can cause low stomach acid because zinc is needed to produce stomach acid. You can take a zinc supplement such as Zinc Picolinate Thorne or Zinc Pure or eat foods high in zinc including oysters, pumpkin seeds, and red meat.

You can also add apple cider vinegar to your meals because it is acidic and helps to increase stomach acid levels. Make sure to dilute with water if you want to drink it before the meal because otherwise it can damage the enamel on your teeth. 

Lifestyle changes that can help improve stomach acid production include chewing food thoroughly and addressing food sensitivities. Supplementation for hydrochloric acid includes supplementing with Betaine HCl. Betaine HCl can be taken before meals to increase hydrochloric acid and help with digestion. For more supplements commonly used to support hypochlorhydria, check out the supplements linked here.

Continuing on through the digestive tract, we have arrived at the small intestine where pancreatic insufficiency or lack of digestive enzymes are the next problem areas to address regarding digestion. Common symptoms of pancreatic insufficiency include abdominal bloating and discomfort, gas, indigestion, or undigested food in the stool. Major diseases that lead to pancreatic insufficiency include chronic pancreatitis, cystic fibrosis, and pancreatic cancer. Other factors that can lead to a lack of enzymes include a diet high in sugar and processed foods, repeated antibiotic use, smoking, aging, and stress. 

In addition to addressing these underlying factors, you can supplement with an enzyme supplement, which contains proteases, lipases, and amylases. Some of our top picks for digestive enzyme supplements include Similase Integrative Therapeutics, Digestive Enzymes Ultra Pure, and Pancreatic Enzymes Thorne. There are even supplements that include both HCl and enzymes if you need both such as Digestive Enzymes Ultra w/HCl Pure or HCL Pro-Zyme Apex. If you would like help navigating these products to make sure you get what you need, please stop into the store or call our staff and they would be happy to assist you. If you have digestive issues and want an accurate depiction of the enzymes in your body, you can ask your health provider to do labs so that you can select the enzyme supplement with the right combination of enzymes for you. 

The other secretion needed for digestion of fats in the small intestine is bile, which is produced and secreted directly into the small intestine by the liver or is stored in the gallbladder and then released into the small intestine when needed. Bile is also necessary for the absorption of fat soluble vitamins (A,D,E,K) so insufficient bile can lead to vitamin A,D,E, and K deficiencies. There are a few reasons why there may not be enough bile secreted into the small intestine including cholestasis, the slowing of bile flow, or the removal of the gallbladder. A few diseases that cause a restriction of bile flow include chronic liver diseases, such as hepatitis, conditions causing high estrogen levels including pregnancy and PCOS, and obstructions in the bile duct such as gallstones. Additionally, the removal of the gallbladder can lead to a bile salt deficiency because there is no place to store bile when the gallbladder is removed. 

Another reason there may not be enough bile secreted into the small intestine is due to insufficient bile production. Some causes for insufficient bile production include a low fat diet, fatty liver disease, gallbladder problems, gut bacteria imbalance, or damage to the GI tract. The body needs fat to produce bile so a low fat diet can impede bile production. Fatty liver can impair the bile production and secretion in the liver. Gallbladder issues can impede bile regulation. Gut bacteria aid in recycling bile, so without enough beneficial gut bacteria, the body may struggle to recycle existing bile, which lowers the amount of bile in the body. Damage to the GI tract can hinder bile absorption. 

A few signs that may indicate low bile production are light colored stool that is similar to cardboard color, trouble digesting fatty foods, and constipation. Bile is responsible for the cinnamon brown color of stool, so when there is no bile or less bile in the stool, it can be a lighter color brown. You can supplement with bile salts or bile acids. Bile acids need to be conjugated with either glycine or taurine to be used in digestion, while bile salts are bile acids that are already conjugated with glycine or taurine. 

TUDCA is a bile salt that is useful for gallstones and low bile production. TUDCA is a good choice for a bile supplement when there is fatty liver, gallstones, need for liver support, and an issue with insulin sensitivity. Ox Bile is a bile acid that is useful for low bile production and gallstones. Some of our recommended picks for bile supplements are Ox Bile 125 and Ox Bile 500 Allergy Research Group. There are also supplements that can support bile production including BileMin Apex and BitterX Quicksilver Scientific. Ox Bile should be taken after meals because it can raise the pH of stomach acid if taken before meals, while TUDCA should be taken on an empty stomach between meals.

You can also improve bile production and flow through diet by making sure to eat enough healthy sources of fats in the diet and eating foods with a cholagogue effect, meaning foods that stimulate bile flow from the gallbladder. Healthy fats to include in the diet are monounsaturated fats such as olive oil, avocado, nuts, and seeds, healthy saturated fats like those from coconut or eggs, and omega-3 from fish such as salmon or sardines. Foods with a cholagogue effect that support the liver and gallbladder include bitter greens, beets, and dandelion greens. 

In the next post, we will end this series on digestion with a discussion mainly focused on bacteria. We will discuss what happens when some of the body’s natural protective mechanisms for bacterial overgrowth, including bile, hydrochloric acid, and enzymes, fail to protect the body leading to bacterial overgrowth in the intestines. We will also talk about some colon pathology, which is the place in the digestive tract where most bacteria live. Until then, make sure to read the previous post for some tips on how to improve your digestion and maybe give some of the supplements we discussed today a try if you are experiencing digestive issues related to the stomach and small intestine. 

References

Anthony, Kiara. (2023). How to Increase Stomach Acid at Home. Healthline. https://www.healthline.com/health/how-to-increase-stomach-acid 

Berg, Eric. (2024). How to Know if You Have Bile Deficiency . Dr. Berg. https://www.drberg.com/blog/how-to-know-if-you-have-bile-deficiency 

Cleveland Clinic. (2022). Cholestasis. Cleveland Clinic. https://my.clevelandclinic.org/health/diseases/24554-cholestasis Cleveland Clinic. (2022). Hypochlorhydria. Cleveland Clinic. https://my.clevelandclinic.org/health/diseases/23392-hypochlorhydria 

Denhard, Morgan. Digestive Enzymes and Digestive Enzyme Supplements. John Hopkins Medicine. https://www.hopkinsmedicine.org/health/wellness-and-prevention/digestive-enzymes-and-digestive-enzyme-supplements 

Microscopic Colitis Foundation. (2025). Low Stomach Acid is a Common Problem. Microscopic Colitis Foundation. https://www.microscopiccolitisfoundation.org/blog/low-stomach-acid-is-a-common-problem

Murray, M.T. & Pizzorno, J. (2012). The Encyclopedia of Natural Medicine: Third Edition. Atria. 

Sunwarrior. (2020). 8 Signs You Have an Enzyme Deficiency: Symptoms, Causes, and Solutions. Sunwarrior. https://sunwarrior.com/blogs/health-hub/signs-you-have-an-enzyme-deficiency 

Zardast, M., Namakin, K., Kaho, J.E., & Hashemi, S.S. (2016). Assessment of antibacterial effect of garlic in patients infected with Helicobacter pylori using urease breath test. Avicenna J Phytomed, 6(5), 495-501. https://pmc.ncbi.nlm.nih.gov/articles/PMC5052411/