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Testing digestive system function

Reviewed by Dr. Sarika Arora, MD

There are times when changing your diet and taking steps to reestablish digestive balance aren’t enough to resolve your symptoms — perhaps you have a bacterial or parasitical infection that is complicating your imbalance, or you may have a long-term gastric dysfunction that has so far been hidden from view.


Your healthcare practitioner can test you for a variety of conditions and offer medical therapy should you find that one or more of these conditions applies to you. We’ve listed some of the most common tests.

Comprehensive digestive stool analysis (CDSA) — available with and without parasitology

Comprehensive digestive stool analysis is a group of tests for evaluating digestive system function, absorption, gut flora, and the colonic environment. This series is indicated for all chronic GI problems, including diffuse and nonspecific GI-related symptoms like indigestion, dysbiosis, constipation, and diarrhea, but is also sometimes recommended for more acute bowel pattern changes and for many systemic diseases. This series evaluates digestion of food particles, nutrient absorption, presence of hidden bacterial or yeast infection, floral imbalance, intestinal immune function, and the adequacy of dietary fiber intake. A stool sample is collected at home and sent for analysis.

Food intolerance/sensitivity testing

Women may want to omit foods such as gluten and dairy that most commonly provoke allergenic or sensitivity responses. But there are plenty of additional foods and food additives, as well as environmental triggers (both from within your body and the world around you), that can trigger digestive symptoms.

Steering clear of foods that provoke symptoms and taking supportive supplements to restore your gut integrity should help most food sensitivities to resolve within 4–6 months, meaning that you may be able to enjoy a food that formerly bothered you. But in some cases, the sensitivity does not go away, and you’ll need to wait longer before including it in your diet again, or, it may be a “fixed” or “true” allergy that will persist throughout your life (these are called “IgE” allergies).

If you’ve closely adhered to your Health Program’s nutritional guidelines, but are still experiencing similar or worsening symptoms, testing for food intolerance or sensitivity is an option you may wish to consider. The following are some of the tests used in functional medical practices to identify food intolerances and sensitivities (IgG).

Potential laboratory/diagnostic tests for food intolerances/sensitivities (IgG)

  • Elimination/challenge dietary protocol
  • IgG RAST to specific foods including milk, egg, or wheat proteins
  • Celiac panel and genetic tests (HLA DQ2, DQ8)
  • Organic acids (specifically by-products of gut flora)
  • Breath testing – lactose, fructose
  • Intestinal permeability testing (lactulose-mannitol)
  • Stool analysis (absorption, digestion, inflammatory markers, microecology)
  • ALCAT testing is a way of identifying whether you are sensitive to any of a variety of potential problem foods and additives, so that you can take steps to avoid them. You can view the available panels and find out more about ALCAT testing at their website: https://www.alcat.com.

Celiac testing

Although considered rare in the past, gluten sensitivity is being identified more frequently today, as awareness of the issue becomes more widespread. Up to 30% of the population has a genetic predisposition to gluten sensitivity and celiac, which cause an inflammatory/autoimmune response in the gut on exposure to gluten, which is a complement of antigenic proteins found in grains belonging to the wheat tribe (Triticeæ, which includes other cultivars such as barley and rye).

We recommend eliminating gluten as part of your Health Program protocol because it helps in reestablishing optimal digestive system function, after which some women will be able to slowly reintroduce gluten-containing foods with minimal ill effect. Others, however, may find they continue to respond favorably to remaining gluten-free once they’ve healed their digestive problems. In those with celiac disease, the most severe form of gluten sensitivity, exposure to foods containing even minute levels of gluten proteins triggers an autoimmune response that damages the small intestine, seriously impairs nutrient absorption, and leads to additional complications. For individuals with celiac, a lifelong gluten-free diet is compulsory.

If you find that reintroduction of even small amounts of gluten cause symptoms to flare, you may be gluten-intolerant or gluten-sensitive. If you suspect you have celiac or gluten sensitivity, have a family history of celiac or other GI diseases, or otherwise have known genetic susceptibility to celiac, you may wish to consider either genetic testing (genotyping) or autoantibody screening (serotyping).

Potential laboratory and diagnostic tests for celiac

    • 3-month gluten elimination trial (“gold standard”)
    • Celiac panel
  • Anti-deaminated gliadin IgG and IgA
  • Anti-gliadin IgG and IgA
  • IgA anti-endomysium antibody
  • IgA and IgG anti-transglutaminase ELISA (tTG)
  • Total IgA (IgA deficiencies 10 times more common in CD)
  • HLA DQ2, DQ8 typing
  • Intestinal biopsy

For more information on gluten intolerance and celiac disease, see our articles:

Pathogens and parasite testing

A multitude of pathogens and parasites can upset healthy digestive system function and cause symptoms in the gut, many of which are common, but others of which are not commonly seen. Certain signs or symptoms may indicate their presence, but the most expedient way to determine whether you are infected is to undergo testing.

Ideally, you will want to have your samples evaluated by a specialist in infectious diseases, as a vast number of organisms exist that could potentially be present. The greater their experience and familiarity with pathogenic organisms that infect the GI tract, the better equipped the pathologist will be to conduct a sensitive analysis that accurately identifies problematic organisms.

A number of labs in the US and Mexico offer screening for yeast overgrowth and the presence of ova (eggs) and parasites, as well as tests that review overall digestive function, including absorption and immune status, as noted above. Further testing may be required to identify specific organisms.

Some of the most important pathogenic organisms affecting digestion are:

  • Helicobacter pylori. A bacterial infection with H. pylori can cause symptoms such as bloating, belching, nausea, and a burning pain in the stomach. Long-term infection can lead to stomach ulcers and inflammation of the stomach’s lining, and is associated with increased risk of stomach cancer. Your healthcare provider can order one of several tests to determine whether you have a H. pylori infection (such as a stool test for the H. pylori antigen), which is generally treated with antibiotics and acid-reducing medications.
  • Fungal dysbiosis / candidiasis. Several molds and yeasts can be harbored in the body and blossom into overgrowth under the “right” conditions. A common example of this in women is the yeast Candida albicans, which is ordinarily found in the digestive tract, but whose numbers can bloom during periods of digestive imbalance. Signs and symptoms of yeast overgrowth can include oral thrush, recurrent vaginal yeast infections, diarrhea, constipation, flatulence, and irritable bowel disease. Candidiasis can be identified through a simple stool test and treated using an antifungal enzyme supplement such as Candex, by following a yeast-free diet, and reintroduction of floral balance with a probiotic supplement containing a competitive, beneficial yeast strain.

Potential laboratory/diagnostic tests for fungal/yeast infections

  • Antibody testing (Candida, specific molds, fungi)
  • Fungal stool culture and stool smear (false negatives are possible)
  • Organic acids: D-arabinitol (false negatives are possible)
  • Nasal swab fungal analysis>
  • Room analysis for molds and fungi (Petri dish culturing)
  • Small-bowel bacterial overgrowth (SBBO). Symptoms of indigestion, especially gas and bloating, but also diarrhea, irregularity and abdominal pain, may signal overgrowth of bacteria in the small bowel. Like candidiasis, small-bowel bacterial overgrowth is a common condition that often underlies maldigestion and malabsorption, but it’s the underlying conditions that favor those organisms that allow these overgrowths to take root, so they must be addressed to ensure the problem does not recur. These are opportunistic infections, so while the organisms themselves may be present, when there is biotic balance between the biofilm colonies lining the bowel, the conditions are such that bacterial or yeast overgrowth cannot take over — or become reestablished.The presence of SBBO can be verified using breath testing.
  • Parasites. Just as our GI tract harbors a multitude of beneficial microbes, many potentially harmful ones exist. “Don’t drink the water” is sound advice for the traveler, but visiting Third World countries and camping out aren’t the only ways to acquire a parasite infection! We are learning that these organisms are quite common, and readily contracted from a variety of sources besides drinking water — infected pets, farm, or other vectors, contaminated foods or surfaces, even walking barefoot on contaminated soil!

Intestinal parasites commonly cause digestive symptoms of diarrhea and abdominal pain, along with flatulence, cramps, blood or mucus in the stools, but also seemingly unrelated symptoms such as fatigue, fevers, chills, and also “systemic” complaints such as rashes, hives, arthritis, and foggy thinking, among others.

You can ask your practitioner to order a panel of tests to identify which organisms are present and treat you accordingly. Some of the more common organisms that can perturb the floral balance and cause tremendous trouble include Giardia, Klebsiella, cryptosporidia, Blastocystis hominis, Entamœba histolytica, and helminths such as flatworms and roundworms. Sending a stool sample to a lab that specializes in “O&P” (ova and parasites) will provide better results than having it sent to a community lab.

Testing for digestive biochemical deficiencies

Good digestion requires sufficient production of a range of biochemicals to assist in the breakdown, assimilation and elimination of nutrients. These include an array of digestive enzymes, regulatory digestive hormones, stomach acid, and bile acids. Women may be deficient in one or more of these as a result of long-term digestive imbalance or other factors that are often genetically-linked. The CDSA panel described above includes evaluation of enzyme and acid sufficiency.

Enzyme deficiencies may be treated through a variety of methods, depending on which and to what extent enzyme levels are low. In some cases, certain foods and herbs can enhance production of enzymes, while in other cases supplemental enzymes may be needed to replace or support what your body currently produces. We recommend that you pursue testing with a functional medicine practitioner to determine whether such deficiencies exist and how best to correct them.

Low stomach acid (also known as hypochlorhydria) is exactly what it sounds like: the stomach produces too little hydrochloric acid, which is needed to prepare the proteins in your food for further breakdown and assimilation in the intestines, as well as serving as a primary mechanism for fending off pathogens that you ingest. Unfortunately, symptoms of low stomach acid are similar to those of excessive acid, and many women are treated with acid suppressants such as TUMS or proton pump inhibitors or before the true problem is identified. This deficiency can often be identified and corrected using a protocol of betaine-HCl supplements. Although it’s available as an over-the-counter supplement, betaine HCl should be taken only under the guidance of a functional medical practitioner, as its inappropriate use can be detrimental to digestive health.

The above are just some of many indicators of GI tract dysfunction and possible progression toward disease. Other concerns that can undergo testing include sufficiency of bile acid production, markers of malabsorption and dysbiosis such as organic acids, markers of oxidative stress in the gut, and highly sensitive markers of bowel inflammation such as calprotectin and lactoferrin. These and more can be carefully analyzed to determine and treat the underlying causes of more serious digestive illness using an array of testing panels in consultation with an experienced functional medicine practitioner.


1 Galland, L., & Barrie, S. [No date of publication listed.] Intestinal dysbiosis and the causes of disease. URL: https://www.healthy.net/scr/Article/?Id=423&xcntr=1 (accessed 02.12.2010).

2 [No author or date of publication listed.] Clinical imbalances handout. Institute for Functional Medicine GI Advanced Practices Module. 02/19–21/2010, Austin, TX.

3 [No author or date of publication listed.] Clinical imbalances handout. Institute for Functional Medicine GI Advanced Practices Module. 02/19–21/2010, Austin, TX.

4 Genova Diagnostics. 2008. Comprehensive Parasitology Profile. URL: https://www.genovadiagnostics.com/files/profile_assets/further_information/parasitology_1pager.pdf (accessed 02.16.2010).

Laboratory websites

  • Aeron LifeCycles Clinical Laboratory
    Tel: (800) 631-7900
  • ALCAT Allergy and Sensitivity Testing
    Tel: (800) 872-5228
  • Diagnos-Techs Clinical and Research Laboratory
    Tel: (800) 878-3787
  • Genova Diagnostics
    Tel: (800) 522-4762
  • Doctor’s Data
    Tel: (800) 323-2784
  • Metametrix Clinical Laboratory
    Tel: (800) 221-4640
Last Updated: July 5, 2021
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