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
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
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
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
1 Galland, L., & Barrie, S. [No date of publication listed.] Intestinal
dysbiosis and the causes of disease. URL: http://www.healthy.net/scr/Article.aspx?Id=423&xcntr=1
2 [No author or date of publication listed.] Clinical imbalances handout.
Institute for Functional Medicine GI Advanced Practices Module. 02/19–21/2010, Austin,
3 [No author or date of publication listed.] Clinical imbalances handout.
Institute for Functional Medicine GI Advanced Practices Module. 02/19–21/2010, Austin,
4 Genova Diagnostics. 2008. Comprehensive Parasitology Profile. URL:
- 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
Heal your your gut naturally
with our Digestive Health Program