Through great struggle comes great learning. My past 6 months have been rough, trying to deal with multiple digestive issues that have multiplied in severity. My routine of identifying the root cause takes me through a journey of trial and error that turns into a learning experience.

It took me going through these issues to realize that digestion is at the root of everything that we feel in our day to day life. It influences our mood, our energy, our drive and so much more. When digestion isn't operating optimally, it's an issue that can make a person extremely self-conscious.

I am going to break down everything that I've learned over the past few months.

Understanding Digestion




First we start in the mouth. This is where digestion starts. Saliva is released in order to begin the breakdown process of the different foods you've eaten. Here's where the importance of mindful eating comes in.

Mindful eating just means that you listen to your body and eat only when you're hungry. Eating when you're hungry and making sure that you do so without any distractions allows for your body to prepare for the digestion of the food you take in.

Smelling your food and looking at your food is where it all starts. Imagine biting into a bright yellow, sour lemon. Notice how your mouth watered at the thought? That's your body's preparation to digest.

When the food has entered your mouth, saliva submersion and chewing begin the digestion process. Ensuring that you coat all of your food in saliva and chew thoroughly allows for ideal digestion. The combination of chewing and saliva creates a bolus of food that is easier to swallow and breakdown further down the digestive process.


After leaving the mouth, food enters the esophagus which is a long tube that connects the mouth to the stomach. Within this tube, the bolus of food moves back and forth on its way down to the stomach.

As the food nears the stomach there is a valve that must open to allow food to enter the stomach. This valve is called the lower esophageal sphincter (LES).


The stomach releases gastric juice (acidic digestive juices), mucus and digestive enzymes. The mucus shields the stomach lining from the acidity of the gastric juices. The digestive enzymes break down fats, carbohydrates and protein. The gastric juice helps to activate the multiple enzymes that are in the stomach and to destroy any parasites that may have entered through the mouth.

While leaving the stomach, the broken down food needs to enter the small intestine but has to first pass through another valve. This valve is the pyloric sphincter.

Small Intestine

The small intestine is where we begin to find bacterial colonies that help to further break down the food that's passing through. These bacteria also protect from infection.

Underneath this layer of mucus and bacteria along the intestinal walls are epithelial cells that separate the small intestine from your blood. There is spacing in between these cells that's just wide enough to allow only the appropriate molecules into your blood.

Large Intestine

The large intestine is the most complex part of the digestive system. You want to know why? In a 1 inch section of your large intestine, there is more bacteria than there has ever been human beings in existence. Your own bodily cells are outnumbered 10-to-1 by bacterial cells!

The bacteria in your large intestine helps to break down food and further extract nutrients. The difference here is that the bacteria in the large intestine provides beneficial bi-products as a result of their own metabolism. It's a symbiotic relationship.

Common Digestive Problems

What you'll come to find with the following digestive issues is that they share common symptoms. It makes it really difficult to pinpoint a cause.

Diagnosing the root cause is something that modern day health professionals fail to do. Typically what happens when someone goes into the doctor's office with digestive issues is that the doctor diagnoses the patient with IBS (irritable bowel syndrome) which has become the "miscellaneous" category of digestive ailments.

Here's an outline of some common Digestive issues...

GERD (Gastroesophageal reflux disease aka. acid reflux)

GERD is an issue (like most other digestive issues) that some people experience without realizing. Common symptoms include: Chest/back pains, burning in the esophagus (throat or chest), asthma symptoms, sour taste in the mouth, and much more.

GERD can make its victims feel terrible after every meal and in-between. Basically, all the time!

Acid reflux (which is similar to GERD) is one of the most wrongly diagnosed and treated disorders. As I had mentioned above, the LES is very important in issues related to acid reflux. The LES actually responds to pH (acidity).

If the acidity is too low, the LES fails to close properly, allowing for gastric juices to flow upward towards the mouth. Gastric juice (or stomach acid) is more acidic than battery acid and is essential to digestion and defense against parasites.

If the production of gastric juice isn't where it needs to be, acid reflux may be the result. Problem is if you go to the doctor, they would probably misdiagnose you with an over production of stomach acid and prescribe you PPI's (Proton pump inhibitors) to slow the production of stomach acid. This can further destroy your digestive system and create irreversible damage.

The condition in which stomach acidity is too low is known as "hypochlorhydria".

Treatment: Treatment for GERD are common with that of hypochlorhydria which is explained below.

LPR (Laryngopharyngeal Reflux)

LPR (aka. Silent reflux) can haunt victims for years. LPR is very hard to diagnose and treat. As the name suggests, LPR is a type of reflux that isn’t necessarily painful. Instead, it causes a cascade of asthma-like symptoms and congestion in the chest.

This can be the most frustrating of the bunch. The reason it's so frustrating is that it can pester those living with it constantly and make them feel like as if they're dealing with asthma. Symptoms include: chest congestion, post nasal drip, coughing, bitter taste in the mouth, constantly trying to clear the throat, wheezing when breathing and troubles breathing deeply.

Treatment: Treatment for LPR are common with that of hypochlorhydria which is explained below.

Hypochlorhydria (Low Stomach Acid)

The ailments mentioned above all share 1 thing in common. Reflux. It seems as though most people are unaware of the true cause of reflux.

Logic dictates that if you have acid reflux, your stomach acid is too high. It's actually quite the contrary. Most cases of reflux actually occur because of a lack of acidity in the stomach, not too much.

This condition is known as hypochlorhydria and affects so many different aspects of digestive health.

Firstly, it ensures that parasites from the outside world are killed upon entry. Most of the harmful bacteria die in extremely high acidity environments. A stomach pH that increases from 1 (very acidic) to 3 (slightly less acidic) can allow for harmful invaders to infect the body.

On top of protecting the body, stomach acid also helps to digest food by activating key enzymes that help to break down nutrients for absorption.

Treatment: Most cases of reduced stomach acid production come from over consumption of carbohydrates (or the wrong types) and bacterial imbalance in the stomach and intestines.

Following a low carbohydrate diet or a SCD (specific carbohydrate diet) can help to alleviate most issues. Also making sure that you're eliminating or reducing any foods that feed bad bacteria is key.

These bad foods include artificial sweeteners (ace-K, sucralose, aspartame), fructose, alcohol, trans fats and sugar in general.

What also seems to help is mindful eating. Chewing your food at least 30 times (per mouthful) ensures that you aren't overusing and abusing the gastric and enzymatic response occurring in your stomach after eating.

Additionally, it's best if you make sure that you are aware of what you're eating (to allow for your system to respond with the appropriate enzymes), coating all of the food in your mouth with saliva and making sure that you're relaxed as you eat. The nervous system can only digest when it's in its relaxed state.

If dietary changes don't appear to work, you may need to supplement temporarily. The supplements you need to take are digestive enzymes and HCL (with pepsin). Follow the recommended label guidelines with the digestive enzymes. With the HCL, you need to determine your required dose.

Start by taking 1 HCL pill after eating. You're going to increase the dosage by 1 pill after each meal until you start feeling a warm sensation in your belly. Do not exceed 7 pills (assuming the HCL dosage per pill is 650 mg).

Once you've found the dosage that gives you a warm sensation, make your regular dosage 1 less than this. Maintain this dose until it starts to produce a warm feeling, at this point you can begin to reduce your regular dosage by 1.

Keep repeating this process till you're at 0 pills per meal. Consider this a gastric acid reset. It's not permanent, it just restarts the engine.

Ulcers & H. Pylori

Another misconception comes in the area of stomach ulcers. Again, the problem is that doctors often attribute ulcers to a stomach acid level that's too high. Digging a bit deeper into this and you'll find that new research is beginning to suggest quite the opposite.

Today, it's believed that the true cause of ulcers is actually, again, low stomach acid. Remember how I said that stomach acid is important in protecting from infections? In the case of ulcers, the stomach pH is too low to protect from one particular strain of bacteria called H. pylori.

H. pylori finds its way through your protective stomach lining (mucin aka mucous that protects the stomach cells from the low pH). The hole that's broken through the mucin, exposes the stomach cells to the low pH of your stomach. Although the stomach pH is lower (which is what gave rise to H. pylori in the first place), it's enough to seriously damage the stomach walls (resulting in ulcers).

H. pylori also thrives off of certain ingredients required to produce HCL. So when the pH is low enough that the H. pylori can survive, the H. pylori actually suppresses the acidity even more. [1] This can further contribute to ulcer, LPR, GERD and other conditions that I will outline below.

With the science beginning to show us an overwhelming amount of evidence for low stomach acid being at the root of stomach ulcers, it's surprising that doctors still prescribe proton pump inhibitors to reduce stomach pH. Doing so destroys digestion to an even greater level, some of which can become irreversible. The more sensible approach would be to test stomach acidity before prescribing any pills. [2]

Treatment: Ulcers can be extremely painful. However, doing the obvious and reducing stomach acid will only allow H. pylori to gain strength, making the ulcers worse. Following the advice given in the hypochlorhydria section above will help to re-balance a proper level of stomach acid. [3]

However, eliminating the H. pylori which is at the root of the problem is where true healing lies. For this, you must eat foods that will not feed them but will instead eliminate them.

Manuka honey has been shown to kill H. pylori effectively. Taking 1-2 teaspoons daily can help you to recover. Ensure that aside from manuka honey, you do not consume any other sugar, even if it's fruit (fructose). Antimicrobial herbs such as oregano (in the form of oil of oregano) can also help to kill off H. pylori. For a more detailed list of oils that are anti microbial, you can visit

Bacterial Dysbiosis

Bacterial dysbiosis. What exactly is dysbiosis? It's an unfavorable balance of bacterial colonies in the gut. Think of your gut as a forest. The proper diversity of a forest is essential to the health of the entire system. Introduce one bad species and the entire system begins to fall apart.

These bad bacteria (or parasites) leach all of the essential nutrient meant to feed the good bacteria and also release toxins into the system. Dysbiosis has been linked to symptoms of depression, anxiety and general mental performance. What most people don’t realize is that more than half of serotonin and melatonin production is produced in the gut. The proper balance of bacteria is so important for the proper production of these essential hormones.

Aside from hormonal balance, dysbiosis can actually influence the body's ability to handle fat. Bacterial balance has been show to influence insulin response and the body's weight set-point (the body weight that the body stays at with any variance in either direction being hard to accomplish).

Aside from a general dysbiosis, people can also experience SIBO (Small Intestinal Bacterial Overgrowth). The small intestine is usually fairly sterile compared to the large intestine which is home to trillions of bacteria. If, for example, the small intestine fails to clear food into the large intestine effectively, bacteria can overgrow within the small intestine.

Symptoms of SIBO include: Bloating, brain fog, nausea, skin problems, depression, diarrhea or constipation, intense cravings, the list goes on and on.

Another parasite that can overgrow in the gut is fungus. Specifically, it's candida, which is a type of yeast. Candida is extremely difficult to combat. It's symptoms are very similar to SIBO as well. Candida can overgrow in any part of the digestive system (ie. Intestines, esophagus, mouth). It causes rashes, bloating, white (cottage-cheese looking) layer on the tongue, wheezing, allergies, chronic sinus infections, intense sugar cravings, etc. It's similar to SIBO but can make you feel like you have any of the conditions listed above so far. Even worse, it can contribute to leaky gut which is described below.

Candida can also enter the blood and become systemic, at which point it can actually be deadly.

The main contributing factors to the overgrowth of any of these parasites are: the use of oral contraceptives, steroids, antibiotics, stressful events, high sugar diets, food sensitivities or intolerances. It's alarming to review the precursors and the symptoms of these parasitic infections because you begin to realize that so many people unknowingly live with these issues. They just accept it and live with it as if it's part of their normal functioning.

Treatment: Bacterial dysbiosis is treated different depending on the type of dysbiosis that's being faced. When it comes to SIBO, you want to eliminate, nourish and re-inoculate the bacteria of the gut.

Elimination involves a few weeks of a good mix of antimicrobial herbs such as cinnamon, clove, garlic, oregano, ginger, pau d'arco, and so many more. Slowly increasing your dosage until you reach the recommended dosages and maintaining that for 3-4 weeks will help to eliminate any of the unwanted bacteria in the intestines. This process will requiring tweaking until you reach a plan that works.

The nourishment of the good bugs in the gut means that you are feeding them food that helps them to thrive. The food that these bacteria thrive off of are soluble fiber, prebiotics and resistant starch. All of these foods are just a form of fiber which you can get by eating legumes, green vegetables, nuts and seeds.

The re-inoculation stage comes near the end of the previous two stages and involves eating probiotic rich foods or taking probiotic supplements. Probiotics are healthy bacteria that contribute to a proper balance of gut bacteria. These bacteria aid in the proper digestion of food. This means reduced bloating, normal bowel movements and improved mood.

Leaky Gut Syndrome

Leaky gut syndrome, better known in the medical community as intestinal permeability, occurs in the small intestine. This conditions has multiple causes and multiple consequences. Symptoms/consequences include: brain fog, acne, new food sensitivities, autoimmune diseases (such as hashimoto's, alopecia, arthritis, IBD, and so many more), allergies, skin conditions, and many more.

The small intestine is lined by epithelial cells which separate the bloodstream from the small intestine. These epithelial cells are also covered with a layer of mucus that further protects from infection and unwanted substances that are not meant to enter the bloodstream. The epithelial cells form tight junctions between one another, with gaps wide enough to allow for just the right particles to enter the bloodstream.

When the mucus layer takes damage to the point that larger and larger particles can find their way through the tight junctions, many of the symptoms listed above start to be seen. Some of the causes of the damage in the small intestine include: undigested food particles (incomplete digestion or food intolerances), SIBO, Candida, infections, gluten (for some people) and dairy (for some people).

Treatment: To heal leaky gut, it is imperative that the root cause is first removed whether the cause is SIBO, Candida, an infection, improper digestion or any other problem. Secondly, making sure that the gut is stable in its balance of bacteria. Doing so will ensure that the gut is protected from any foreign parasites.

Once the chance of recurrence is reduced, the gut can be healed. To do this, healing must be encouraged using collagen protein. Collagen can be found in different powder form supplements or bone broth. Two amino acids in Glycine and Proline are specifically helpful in the restoration of tight junctions in the gut. Other supportive supplements include: L-glutamine, Quercetin, Licorice root, Omega-3 and Vitamin D.


It's clear that there's so many potential issues that you could run into with digestion. Maybe you're already going through it.

For me, digestion seems to be the root cause of so many of my fitness issues. Eating too fast, a past full of junk food and chronic stress have all contributed to the difficulties I've faced in my health and fitness journey. Over the past 3 years (when I started my health and wellness journey) I've found it extremely difficult to control cravings and lose fat around the waist. Dysbiosis in my gut along with negligence when it comes to cheat meals may be the reason for my lifelong struggles.

Can you see the pattern? The central cause of most of the things I listed above is low stomach acid. However, the low stomach acid may cause an overgrowth of bad bacteria which can further interfere with the production of stomach acid through multiple different mechanisms, whether that's SIBO, H. pylori, candida or even leaky gut syndrome.

This article was not meant to cover everything. This was only meant to cover the conditions and processes that I've looked into by trying to solve my own issues. Let this shed light on some things you might not have known, and allow you to research it in more detail.

Hopefully you can find some valuable insight into some problems that you might be facing. Identify and eliminate the root cause. Discover New potential.

For the original article, visit:


[1] NCBI. "Molecular hydrogen as an energy source for Helicobacter pylori". [Online]. Available:

[2] Chris Kresser. "The Dangers of Proton Pump Inhibitors". [Online]. Available:

[3] NCBI. "Bacterial killing in gastric juice--effect of pH and pepsin on Escherichia coli and Helicobacter pylori". [Online]. Available:

Published by Alaa Allen Elbanna