Saul Marcus, ND - Naturopathic Doctor

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Functional Lab Tests For The Digestive System

The problem with conventional lab tests

If you go to a primary care doctor, or gastroenterologist with digestive symptoms, they may recommend one of the following lab tests:

When conventional test for the gastrointestinal system can help

There is nothing wrong with any of these tests, as long as they are used in proper context.

For examples, a colonoscopy can be used to diagnose colon cancer, inflammatory bowel disease, or causes of gastrointestinal bleeding.

An abdominal ultrasound can be used to diagnose inflammation of the gallbladder or appendix in case of abdominal pain.

Problems with conventional tests

Conventional tests are often costly, invasive, and don't diagnose many underlining causes of digestive symptoms. These basic causes are intestinal dysbiotis (and imbalance in the types of bacteria living there), candida, food allergies, inflammation, low secretory IgA, poor immune function, and parasites. The effectiveness of imaging and colonoscopy for diagnosing parasites depends on the size of the parasite.

At times conventional tests may be somewhat helpful in diagnosing these problems, but are not always the ideal tests.

Often people may be issues which can be picked up on "functional tests" for the gastrointestinal system, yet not be picked up with conventional tests.

Functional lab tests

A functional problem is not a disease in itself. Rather, this is an underlining issue which over time may cause symptoms, and later lead into a disease. .

Bacterial and yeast culture

A stool culture for bacteria and yeast can quantify amounts of certain dysbiotic organisms such as candida, Klebsiella, E. coli, Streptococcus and more. Besides diagnosing the problem, this simply test is also useful in tracking treatment.

Inflammatory markers

Just as there are blood markers for inflammation such as C reactive protein and homocysteine, there are also stool markers for inflammation in the GI system.

Intestinal Lysozyme: marker of colonic inflammation
Alpha Anti-chymotrypsin: marker of GI inflammation including in the small intestine
Lactoferrin: inflammatory marker which can help to differentiate inflammatory bowel disease (Chron's or Ulcerative Colitis) from other GI system disorders.

Secretory IgA

Immunoglobulins are a major part of our immune system. In blood, the major immunoglobulin is IgG. Along the mucous membrane of our GI tract sIgA (secretory IgA) is the major immunoglobulin.

sIgA is the immune system's first line of defense. If sIgA is too low, the immune system can't easily target and eliminate antigens in the GI system. This allows bacteria and antigens to cross the gut lining and trigger other kinds of immune responses (IgG reactions).

The page on autoimmune hypothyroidism has much more information on this phenomenon.

This leads to a deregulation in the immune system, whereas in some ways it's under active, and in other ways it's over active. Many immune system disorders ranging from allergies, asthma and auto-immune disease are affected by sIgA.

sIgA is lowered by dysbiosis and stress. Some people also have genetically a secretory IgA deficiency (which can be tested for through blood).

Stool tests for sIgA levels can be a big step in resolving many health issues which begin in the gut.

There are also blood tests for sIgA which are useful as well, but don't give the same information. The blood will help diagnose genetically low sIgA, which the stool tests will show low sIgA in the GI system which does not need to be a genetic problem.

Food allergies

An inflammatory reaction to food can cause GI inflammation and cause other digestive symptoms. In addition, other digestive problems (such as those mentioned in this page) can lead to gut permeability (also called "leaky gut") and a propensity towards food allergies.

The most common allergies are to wheat, corn, soy, eggs and dairy. Food allergies can be tested for via IgG blood tests, or IgA stool tests.

Eliminating allergies is an important step in reversing digestive symptoms.


Parasites are and often under diagnosed problem.

Common parasites include:

Blastocystis hominis - estimated 2.6% of US population infected. About 50 - 80% of those infected will present with symptoms, and often diagnosed with "Irritable Bowel Syndrome."

Clostridum difficile - estimated 5% of US population infected. Often causes diarrhea.

Entamoeba coli - estimated 4.2% of US population infected.

Toxoplasma gondi - estimated 40 - 50% of US population infected. Causes multiple symptoms including brain cysts leading to behavioral disorders, muscle cysts, depression, insomnia and reduced stress tolerance.

Entamoeba histolytica - causes episodic diarrhea or perianal itch causing colon ulceration. May be locally invasive, causing liver and lung abscesses.

Trichinella spiralis - tissue worm, causing abdominal cramping, nausea, diarrhea and muscle soreness and pain leading to fibromyalgia, edema of the upper eye lids or fever.

Ascaris lumricoides - roundworm. The most common worm infection in the world. Causes nutritional deficiencies, reduced liver and pancreas function, intestinal colic, diarrhea, dyspepsia and spasmodic cough.

How are parasites diagnosed?

  1. Microscopy. This is the most common method, where a stool sample is examined under a microscope for visual evidence of a parasite. It's best to have such tests done by a lab which regularly does parasite tests and knows what to look for.

  2. Elisa IgA. Some parasites can be tested for by doing and Elisa stool test for antibodies to the parasite.

  3. DNA analysis is another newer method for diagnosing parasites.

There are numerous companies that have stool panels for parasites which include: diagnos-techs, doctors data, Genova diagnostics and metametrix.