Digestion Issues

Gut issues “affect 60–70 million people in the United States, cause 13% of all hospitalizations, provoke approximately 50 million physician office visits, and cost about $107 billion (direct + indirect costs).”

Gut issues are so common that people I work with believe that gas, bloating, constipation, diarrhea, GERD, etc. are normal! As uncomfortable as those may be, the real concern is that a “broken” gut can lead to unsuspected health issues.

What constitutes a well-functioning gut?

A great digestive system would be one with the following characteristics:

  • No gas, cramping, pain, heartburn, bloating, or diarrhea
  • No undigested food, mucus, or blood in the stool
  • Transit time of 18-24 hours (test with charcoal or beets)
  • No obnoxious smell (might need to verify with your spouse!)
  • Brown color (green is okay if lots of greens are consumed)
  • Stool that forms a nice log shape or a lazy S that sinks to the bottom of the toilet
  • Minimal residue on the toilet tissue

What conditions affect my gut function?

Good digestion starts with the thought of food which stimulates digestive juices. Saliva release begins the digestive process of both starch and fats. After you thoroughly chew your food, it is sent to the stomach, where it starts to break it down. It is then slowly released to the intestines to “wring out” nutrients. Finally, waste products are collected to leave the body. 

Therefore, to unravel gut issues, we literally need to address function from our mouth to the toilet bowl. 

Please note that digestion can be affected by almost anything:  diet, chemical exposure, pathogens, inflammation including neuroinflammation, autoimmune conditions, thyroid, stress and adrenal disorders, vagus nerve, fat assimilation issues, dehydration, microbiome issues, neurotransmitters, etc.

How does poor gut function affect my health?

Systemic Health

If we can’t effectively breakdown our food, we will not be able to assimilate the nutrients needed for basic functions such as making energy, performing detoxification, repairing our cells, supporting immune function, generating hormones, etc.-basically everything!


The biggest impact to our health may be may the direct effect it has on our immune system. Turns out that the majority of our immune system resides in our gut which makes sense considering it is a direct link to the outside world.

Pathogens or issues with food can generate a great deal of inflammation—both inside and outside of our gut.

Leaky gut

When we consume foods that our bodies are sensitive to or if we have an infection, it can create an inflammatory response. Inflammation can then lead to the formation of “leaky gut” or unintended openings in the intestines. This allows food to leave before being fully processed. The body then considers these “fragments” as foreign and mounts an immune response.

Sometimes the food particles are similar in structure to various tissues in the body which causes the immune system to mistake the tissues for the offensive food. This can lead to autoimmunity against that tissue or organ. For example, gluten and Hashimoto’s thyroid are highly associated in the medical literature.

Read more about leaky gut here.


A healthy gut has a diverse microbiome that helps keeps our barriers intact; supports immune function by stimulating the production things such as Secretory IGA (SigA) immunity and T killer cells; and helps breakdown our food and generate essential vitamins. Issues with dysbiosis or overgrowth of pathogens, limits these normal gut activities.

Read more about microbiome here.

What are some common symptoms of gut issues?

  • Gas
  • Bloating
  • Stomach pains and cramps
  • Undigested food in stool
  • Diarrhea/constipation
  • Burning and GERD
  • Mucus and phlegm
  • Food reactions

Issues can also include:

  • Headaches
  • Weight issues
  • Liver and detoxification issues
  • Cardiovascular issues
  • Neuroinflammation
  • Blood sugar issues
  • Adrenal and thyroid issues
  • Hormone issues
  • Mitochondria issues
  • Detoxification
  • Autoimmunity
  • Fatigue
  • Hives
  • Aches, pains, and swelling throughout body
  • Depression
  • Anxiety
  • Bone loss
  • Arthritis
  • SIBO
  • Amd more….

What is the best way to support gut health? The 4R Protocol

While we address root cause, we apply a “4R” protocol to help detect and alleviate GI problems.

This includes removing offending foods/environmental factors and detecting/eradicating infections, replacing whatever the body temporarily needs to help breakdown and digest food, repairing an inflamed gut, and reinoculating with healthy bacteria.

1. Remove

Genetics, environment, diet, or overgrowth of gut pathogens (viral, bacteria, fungal, parasite) can all play a role in affecting gut function.


Before we get into food, I want to point out that stress can really hinder digestive function. Digestion is a parasympathetic process, which is to say that it works best when the body is nice and relaxed with nothing critical to do.

So if you eat while you’re fighting with your spouse or you’re angry about the guy who cut you off in traffic—or even if you eat while you’re working—you may not be able to effectively digest your foods. 

Just some food for thought. When I take an evening walk and stop to admire my neighbor’s impressive garden, I often see a flicker of candlelight coming from her dining room. Each and every night, she makes dining a special event. With her favorite music playing in the background, she sets her table with care and makes sure that meal is not only prepared with fresh ingredients, but filled with beautiful colors as well. “It makes our meals together something special,” she says. “The day is done, and we are home together nourishing our bodies, our health, and our relationship. What could be better?”

Read more about stress here.

Food issues

Just because a food is considered “healthy”, it doesn’t mean it may not still be reeking havoc on your health.

Individuals can have issues breaking down foods in general, issues with specific foods or food families, or systemic issues with oxalates, glutamates, salicylates, histamine. glyphosates, etc.

Known food issues

If you have an issue with a particular food, it is important to understand why. For example, maybe you’re pretty sure you have an issue with celery.

  • Is it an immune response to the food or are you just having a problem breaking it down?
  • Do you have a problem with the entire food family—in this case, Apiaceae? That might be the case if you also have problems when eating foods such as parsley and carrot.
  • How you feel when you consume dark greens or nuts? If those foods also bother you, could your issue with celery be related to oxalates? If so, why? Are you forming oxalates because of yeast overgrowth, high vitamin C consumption, genetics, or some other reason?
  • Or do you get skin, respiratory or some other response? If so, might there be an issue with histamine producing foods?
  • Or do you just have an issue when it is cooled or maybe combined with something like onions?
Unknown food issues

Most folks think of food allergies only as rashes, hives, or asthma, but the most common food allergies don’t cause an immediate reaction or even show up on regular allergy test. Instead, they often lead to undetected inflammation—which compounds each time you eat the questionable food.

The good news is that most food sensitivities are usually not permanent and normally respond well to an elimination period and rotation diet.

You can learn more about food sensitivity and common problematic foods here.

Elimination diet

The best way to deal with food issues is by removing well known allergenic foods for a period of 4-6 weeks and then adding them back in a systematic manner. This break allows your immune system to relax and recover so that when you are ready to put it back to work, it responds appropriately and with some enthusiasm!

And during the process, you will have gained first-hand knowledge of how foods affect you.  Learn more about the most effective therapeutic elimination diets here.

Pathogenic load

If dietary changes don’t provide the desired effect, we can address potential pathogenic load. You might want to consider testing which looks at both beneficial bacteria and pathogens as well as basic blond testing which looks at immune system dysfunction. 

Keep in mind, it is best to address leaky gut issues first before attempting to eradicate infections. This will help minimize overloading the immune and detoxification systems.

2. Restore

The next step is to restore anything the gut may be lacking to breakdown and assimilation of our food.

To help normalize gut function , we often use temporary supplementation to help restore enzyme levels, support gallbladder function, restore gut acidity, etc. Please work with your healthcare provider for a personalized approach.


Low HCL creates a three-fold problem. First, foods can putrefy leading to leaky gut. Second, we cannot effectively breakdown proteins which minimizes our “pool” of amino acids need to create proteins—the very ones required our immune system to function. Third, without sufficient acid, we can’t sterilize our food to kill potential pathogens.

You can read more about HCL here.

Digestive enzymes

The release of HCL signals our intestines that food is on the way to be processed. Without this signal, digestive enzymes aren’t released from the pancreas. And without these important digestive cofactors, we cannot effectively assimilate our nutrients,

What causes pancreatic insufficiency?
  • Overeating (this overloads the system)
  • High alcohol consumption
  • A diet too high in only cooked foods that rely too heavily on pancreatic enzymes
  • Eating too many devitalized foods that lack zinc, manganese, vitamin B6, and magnesium
  • Low HCL (which doesn’t signal the release of enzymes)
  • Insufficient protein intake (which will not provide the pancreas with the amino acids it needs to create enzymes)
  • A diet that is deficient in fiber and too high in sugar
  • Metabolic acidosis (this happens when the body is trying to conserve bicarbonate produced by the pancreas to help reverse an imbalanced internal environment)
  • Spasms in the duodenum (this may cut off the supply of bicarbonate)
  • As we age, we start to lose the ability to make sufficient enzymes. According to the Journal of Clinical and Experimental Gastroenterology, pancreatic secretion in the elderly is reduced by 50%.

Gallbladder support

Our gallbladder stores bile for breaking down fats.

The ingestion of fat causes the release of a hormone which signals he gallbladder to squirt bile into the small intestine, where it helps break down fats–much like laundry or dish soap.

In addition, our liver uses bile to filter toxins and send them out of the body, so if we can’t create and get bile to where it needs to go, our bodies can become toxic.

Issues with the gallbladder function may allow fats to linger and go rancid, a situation that may lead to inflammation, infection, and gallstones.

What causes gallbladder issues?

Eating too many of the wrong fats may overwhelm gallbladder function. But avoiding fats also creates issues. Limited fat consumption means that the gallbladder works less frequently, which can lead to bile thickening. An analogy might be a turkey baster filled with fat that sits for several weeks.

Additionally, as we age many folks, especially women or those with thyroid disorder, may develop gallbladder issues. 

Finally, there are also some folks with genetic issues that can affect fat assimilation.

How can we support gallbladder function?

A great food for gallbladder health is beets—the betaine they contain helps stimulate bile flow. Other supportive foods include apples, ginger, and bitters.

Consuming moderate amounts of good fats like olive oil, nuts, butter, etc. may help avoid bile thickening.. In addition, phosphatidylcholine may help support the movement of bile.

Those who have had their gallbladders removed may require supplementation to support the processing of dietary fat.

Motility support

Motility issues, which include irritable bowel syndrome (IBS) and constipation, affect 25–55 million people per year. Motility issues can lead to gut disorder known as Small Intestine Bacteria Overgrowth or SIBO. Folks with this condition cannot effectively assimilate their nutrients and often experience extreme gas, bloating, and malnutrition.


Our enteric nervous system (ENS) is considered our second brain and is responsible for regulating the behavior of the gut. You probably wouldn’t expect to see serotonin, a neurotransmitter, in regards to digestion, but with than more than 90% of the body’s 5-HT is located in the gut, it plays a large role.

Serotonin is an important signaling molecule that initiates peristaltic movement, which is the normal rhythmic movement of the gut muscle that helps move contents along the way. It also transmit information back to the central nervous system (CNS), and regulates digestive secretions and the perception of pain or nausea.

If we have issues with diet or the cofactors required to produce serotonin (which include: oxygen,  B vitamins, iron, methylation, etc.), our digestion may be impaired. Some folks have genetic defects or SNPs, that can affect the production of serotonin and may benefit with support.

Vagus nerve

The vagus nerve is  also involved in peristalsis by signaling the muscles in your stomach to contract and push food into the small intestine. A damaged vagus nerve can’t send signals normally to your stomach muscles. 

There are exercises that can help restore vagal tone such as deep breathing, gargling, etc. You can learn more here.


We all know we should be consuming lots of fiber to help move food gracefully through our digestive system. Plant fibers (called cellulose) consist of chains of glucose held together by indigestible links. Since we cannot break down these links, fiber moves through the gut undisturbed. This slows down the digestive process and provides bulk to our stools which helps generate enough downward pressure to allow us to have good bowel movements.

In addition, consumption of good dietary fats and hydration are essential. Put simply, they can help soften the stool to provide more mass to create greater downward pressure to aid in constipation.

Brain Issues

Those with issues with reduced brain function either due to injury, neuroinflammation, leaky brain, etc., may have issues with motility.

3. Repair

This step goes right into “sealing up” a leaky gut and calming down inflammation with things such as short chain fatty acids, aloe, marshmallow root, etc. This step often brings dramatic relief to those with chronic gut inflammation. You can read more about leaky gut here.

4. Reinoculate

Since bacteria are at the heart of our immune system, we may need to restore diversity to our microbiome through the consumption of fiber and fermented and prebiotic foods or a probiotic supplement.

Fermented foods been around since ancient times and are found in cultures around the world, from Roman sauerkraut to India lassi to Korean kimchi. Just as fermented yeasts are used to make wine, sugars and starches are fermented with lactic acid to produce bacteria such as lactobacillus and bifidobacteria. Other sources include yogurt, natto, kefir, kombucha, tempeh, and pickles, to name a few.

You can read more about probiotic food and fiber here and the microbiome here.

How can I test for gut issues?

Functional Medicine is all about a personalized approach which makes testing important–since there can be many reasons why your gut function is not optimal.’

Leaky gut

There are advanced functional medicine tests to determine if your gut is leaky. Cyrex Laboratories has Intestinal Antigenic Permeability Screen that is especially good.

In our office, we start with Functional Blood Chemistry and look for patterns of markers that trend toward leaky gut.

Infection/gut function

GI Map DNA stool testing is used to determine beneficial and pathogenic load. It also reports on enzyme function, gluten sensitivity, fat absorption issues, and histamine and intestinal damage.

Food sensitivity

Testing for food issues is highly questionable unless is it looks directly at antibodies generated by eating offending foods. In addition, foods should be tested in both their raw and cooked states as the proteins change with processing. Testing might be a good option for those unsuccessful with the elimination diet or for folks with specific autoimmune conditions who need to uncover potential reactions to specific foods that might upregulate their condition.  Cyrex Labs Array 3, 4, and 10 are recommended.


You can determine motility issues simply by examining your stool after consumption of beets or charcoal. The color should be seen 18-24 hours after ingestion. 


The best and most cost effective way is an HCL challenge test in which acidity is slowly increased to determine how symptoms are affected.

The Heidleburg Capsule test requires swallowing and recovering a capsule to obtain pH info.

In our office, we start with Functional Blood Chemistry and look for patterns of markers that trend toward HCL dysfunction as well as potential underlying cause.

Getting help shouldn’t be difficult!

Contact us for your free 15 minute consultation.

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