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GI Specialty Lab Testing 101: Testing, Results Interpretation, Supplements

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GI Specialty Lab Testing 101: Testing, Results Interpretation, Supplements

It's estimated that 60-70 million people in the United States have some type of digestive disorder. The gastrointestinal (GI) tract encompasses the stomach, intestines, mouth, esophagus, and accessory organs. This article will walk through the digestive system, discussing the functions at each location. We'll then discuss testing for different parts of the digestive system and supplements that can help.


What is The Digestive System?

The GI tract can be compared to an assembly line, with workers in each section doing a specific job that contributes to the function of the GI tract as a whole.


The digestive process begins with the smell or sight of food. Salivary enzyme production begins, continuing when food enters the mouth. The mixture of food with salivary enzymes allows the food to be broken down and allows for taste receptors to be activated, resulting in taste. Lastly, the saliva has antimicrobial properties, hopefully killing off any pathogen that may enter.


The esophagus will continue to moisturize the food. This is also the first location of peristalsis, which is defined as a wave-like movement that propels food forward. In this case, peristalsis takes food into the stomach.


Stomach acid and enzymes mix with food, producing a liquid mixture called chyme. The stomach also produces Intrinsic Factor, a hormone necessary to absorb vitamin B12 in the small intestine. The stomach will also absorb certain fat-soluble substances, alcohol, and aspirin. Peristalsis moves chyme into the small intestine.

Accessory Organs

The liver, gallbladder, and pancreas all aid in digestion. The liver makes bile salts which aid in the digestion of fats. The bile salts are sent to the gallbladder, where they are excreted into the small intestine when fats are present. The pancreas also produces enzymes, such as amylase, lipase, and elastase, that are necessary for digestion.

Small Intestine

The small intestine is made up of three different parts: the duodenum, jejunum, and ileum. Hormones released from the duodenum will cause products from the above accessory organs to be released. This process is called chemical digestion. The chyme then moves into the jejunum, where muscular contraction causes the mixing of chyme with the digestive juices. The mucosa, or lining of the intestinal wall, is also active. The mucosa contains many glands that release more digestive enzymes, mucus, and a small amount of microbes, aiding in the further breakdown of food. Once the food has been broken down to a sufficient amount, absorption of nutrients, including vitamins, minerals, and breakdown products of food occurs via permeability in the lining of the small intestine wall. This process of digestion and absorption also occurs in the ileum. Once chyme reaches the end of the ileum, a valve called the ileocecal valve will open, allowing chyme to enter the large intestine. The valve functions to inhibit microbes from the large intestine from entering the small intestine.

The table below shows the various nutrients absorbed throughout the small intestine.

Nutrient Absorption in the Small Intestine

Large Intestine

The large intestine, or colon, houses the microbiome, a collective group of organisms including bacteria, fungi, and viruses. There are so many microbiomes in the large intestine that they actually outnumber our genes by 150:1. The microbiome has numerous functions, including the further breakdown of food and absorption of nutrients, creation of nutrients, elimination of toxins, production and modulation of immune cells, neurotransmitters, and other signaling molecules, and creation of butyrate, the primary fuel source for colonic cells. As these processes occur, chyme is moved towards the rectum, where its final step of excretion occurs in the form of stool.

Functional Medicine Labs to Test for Each Section of Digestion


Small Intestine Bacterial Overgrowth (SIBO) occurs when the microbes from the large intestine move into the small intestine, where they wreak havoc, causing improper digestion and absorption and releasing inflammatory molecules, and more. A SIBO test will have the patient drink a sugar solution and then take breath samples for up to two hours after. The lab assesses the breath samples, looking for different gasses that the bacteria would produce if they came in contact with the sugar solution the patient drank.

Parts of the GI assessed: Small intestine, large intestine.

Comprehensive Stool Test

A comprehensive stool analysis, such as GI360 by Doctor’s Data, shows markers of digestion and absorption, including various enzymes. It also deeply examines the microbiome, including beneficial, opportunistic, and pathogenic microbes. Lastly, this test shows immune and inflammatory markers.

Parts of the GI assessed: stomach, small intestine, large intestine, pancreas, liver, and gallbladder.

Leaky Gut Panel

This panel assesses markers for the quality of small intestine permeability, also known as Leaky Gut. As discussed above, digestion and absorption should only allow the absorption of molecules when they're properly broken down. With increased permeability, molecules not completely broken down may pass through into the bloodstream, possibly leading to chronic inflammation and food sensitivities, amongst other problems.

Part of the GI assessed: small intestine.

Liver Panel

The liver makes bile which is then stored and released by the gallbladder. Therefore, liver and gallbladder functioning is essential to digestive health. The gallbladder is connected to the liver, and thus irregular functioning of one organ often interferes with the other. A liver panel will show liver enzymes and other liver products that can give insight into liver and gallbladder health.

Parts of the GI assessed: Liver and gallbladder.

Amylase, Lipase

Amylase and lipase are two enzymes released by the pancreas that aid in the digestion of macronutrients. Testing can reveal elevations or deficiencies in these enzymes, which can signify that the pancreas is malfunctioning. Amylase and Lipase are both tests offered by Access Medical Laboratories.

Parts of GI assessed: pancreas.

Micronutrient Testing

A micronutrientcan be helpful, as vitamins and minerals are necessary for many stages of the digestive process. B vitamins play a role in the health of the intestinal mucosa and the development of different cells in the intestines. Vitamins A, D, K, B2, B3, and C positively impact the microbiome by improving diversity. Zinc carnosine positively impacts the mucosal lining of the GI tract.

Additionally, systemic levels of nutrients are completely dependent upon the gut via two mechanisms. The first mechanism is the process of digestion, where food needs to be broken down properly, and absorptive mechanisms need to be working correctly in order for nutrients to be absorbed. The second mechanism is the creation of certain vitamins by the microbiome, where dysbiosis may alter the rate of synthesis of those vitamins. Thus, checking micronutrient levels may be necessary if GI issues are suspected.

Parts of the GI assessed: all.  

Other Lab Tests to Check

Hormone Panel

Hormone levels may be influenced by gastrointestinal functioning. Estrogen levels, specifically, are influenced by a collective group of bacteria in the microbiome called the "estrobolome." These bacteria are responsible for packaging estrogen metabolites from the liver and putting them into the stool for excretion. However, dysbiosis in the estrobolome may cause the bacteria to send the estrogen back into the bloodstream and may lead to higher estrogen levels. This can occur in both men and women.

Food Sensitivities

Food sensitivities can be a result of increased intestinal permeability. If foods are not broken down correctly, and large food particles transfer into the bloodstream, the immune system can form antibodies to the foods, as they view them as a foreign invader.

Supplements That Benefit Each Digestive Organ

Marshmallow root

Marshmallow root is a botanical that has been used for thousands of years. Marshmallow root contains mucilage, a substance that can soothe the esophagus and stomach lining. Because of this, marshmallow root can be helpful in Gastroesophageal Reflux Disease (GERD), sore throats, coughs, indigestion, and more.

Milk thistle

Milk thistle is a botanical that is beneficial for the liver. Milk thistle contains silybin and silymarin, two phytonutrients that have antioxidant actions on liver cells, protecting them from damaging free radicals. Milk thistle has also been shown to benefit the gallbladder, reducing the risk factors that lead to gallbladder diseases.

Digestive Enzymes

Digestive enzymes, as discussed above, are made by the stomach, pancreas, and liver. Supplements containing digestive enzymes vary; some contain only a single type of digestive enzyme, and some may contain all of them. If digestive markers on comprehensive GI testing are low, or amylase, lipase, or liver panel results are off, digestive enzymes may be warranted. Dosages will vary based on the digestive enzyme type and the supplementation goal.


The most common amino acid, l-glutamine, is essential for small intestine health as it is the primary fuel source of enterocytes or small intestine cells. It can also aid in healing damaged tissue of the digestive tract, especially the oral mucosa when used as a mouthwash. Duration of supplementation is at least five days, with a 15-45g range of dosage.

Zinc carnosine

Zinc carnosine has the potential to heal damaged mucosa found in the mouth, esophagus, stomach, and small intestine. It has been used for oral mucositis (oral inflammation), ulcers, GERD, and Helicobacter pylori infections.


Probiotics are supplements that contain strains of beneficial microbes that should be found in a healthy microbiome. The most common species of microbes are the bacteria Lactobacillus and Bifidobacterium, although most probiotics contain several other microbes. It has been shown that the more diverse and populated a microbiome is, the healthier it is. Probiotic supplements will have varying strains and dosages.


Prebiotics are insoluble fibers that feed the microbes in the microbiome. By consuming these probiotics, microbes create short-chain fatty acids (SCFAs), which aid in digestion and absorption, lower inflammation, and lower permeability in the small intestine, amongst other things. Systematically, SCFAs can increase calcium absorption in bones, enhance memory and learning, and more. A five-gram dosage is ideal for enhancing the microbiome.


Knowing the function of the entire GI tract, it’s no wonder Hippocrates once said, “All diseases begin in the gut”. Each section has its own purpose and importance that affects not only gastrointestinal health but the whole body's health, as all tissues require nutrients that are digested and absorbed through the digestive tract. Many tests can be used to assess different parts of the GI tract, and supplements can target each section as well.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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