There are three general categories of lab tests to consider as part of your overall strategy to address the root causes of autoimmunity:

  1. a microbial pathogen stool test
  2. a SIBO breath test
  3. a food allergy & sensitivity test

None of these tests are necessary, but they can streamline the healing process by helping you to identify what to focus on when it comes to figuring out your optimal diet, probiotics, and other supplements.


1. Microbial Pathogen Tests

The most useful laboratory test is likely a stool test for microbial pathogens. This type of test is the best way to determine whether you may have an overgrowth of any of the specific bacteria that appear to play a role in driving autoimmune disease.[i]

In the context of psoriasis and arthritis, the species of bacteria that we are most concerned with include:

  • Escherichia coli
  • Klebsiella pneumonia
  • Enterococcus faecalis
  • Proteus mirabilis
  • Streptococcus pyogenes

These bacteria produce immune-activating toxins such as lipopolysaccharide, along with bacterial proteins that may confuse the immune system by closely resembling our own proteins. They have the net effect of encouraging the immune system to shift towards a more inflammatory state, by promoting the proliferation of Th17 helper T cells, which play a direct role in autoimmunity.  (Overgrowths of Candida yeast may also drive signficant inflammation and this can often be detected by the same stool tests that are used to investigate pathogenic bacteria.)

Knowing that you have an overgrowth of a particular species can help you choose strategies that are most effective at suppressing that species. A low-starch diet is particularly helpful for those with Klebsiella overgrowth, for example, while those with an E.coli overgrowth may be especially likely to respond well to the probiotic Mutaflor (as discussed further in the book).

In the United States, microbioal pathogen testing options include:

GI-Map is likely the most sensitive test for detecting the bacterial species involved in autoimmunity, because it relies on detection of DNA, so bacteria can be identified even if they do not grow well in the laboratory.  (Genova’s GI Effects panel also includes some DNA-based detection of certain bacterial species, in conjunction with other methods).

Although GI-Map is the likely the best choice for the specific detection of pathogenic bacteria, the Comprehensive Digestive Stool Analysis tests offered by Genova and Doctor’s Data have other advantages. These tests can detect other factors, such as metabolic markers, enzyme insufficiency, parasites, and the level of gut inflammation.

All of these tests are fairly expensive (around $350-$500), but can often be ordered directly without a doctor’s prescription through various websites, such as Direct Labs.  In addition, the GI-Map test can be ordered through:

Genova’s GI Effects test can also be ordered through Forrest Health.

For those located outside the United States, these same tests can often be ordered through local services, who then coordinate with the labs in the USA.  For example, in the UK, tests can be ordered through:

Although you do not need a doctor to order these tests (other than states such as New York), you may still find working with a functional medicine practitioner is helpful when it comes to interpreting the results. For a directory of physicians familiar with analyzing and treating problems identified through microbiome analysis, see the Institute of Functional Medicine (www.ifm.org).

2. SIBO Breath Tests

Beyond the specific inflammatory bacterial species that are listed above, there is also evidence that a general excess of bacteria in the small intestine can trigger the autoimmune process.  This scenario, termed Small Intestinal Bacterial Overgrowth (SIBO), is a recognized medical condition.

Recent studies have found that SIBO is present in a significant proportion of patients with psoriasis, [ii] rheumatoid arthritis, [iii] and fibromyalgia. [iv]  In one small recent study of patients with both SIBO and psoriasis, treating the bacterial overgrowth with a short course of antibiotics dramatically reduced the severity of psoriasis. [v]

SIBO becomes an even more likely culprit if, in addition to psoriasis or arthritis, you also have the other common signs and symptoms of the condition. SIBO often manifests as either chronic constipation or diarrhea. It is found in up to 80 percent of people with irritable bowel syndrome and is now regarded by some experts as the most common cause of IBS.[vi] Other classic symptoms of SIBO include multiple food sensitivities, histamine intolerance, nausea, bloating after meals, abdominal pain, eczema, and rosacea.

If you have any of these common symptoms of SIBO, or a major risk factor such as celiac disease, endometriosis, or a history of food poisoning or abdominal surgery, it may be worth taking a breath test to help determine if SIBO is a contributing factor for you.

The SIBO breath test involves drinking a lactulose and/or glucose solution and collecting breath samples over several hours using an in-home kit. (The lactulose test is typically preferred because it is better at detecting the most common forms of SIBO, although it can miss some cases that are detected only by a glucose test).

SIBO breath tests are far from perfect: they are sometimes difficult to interpret, and miss many cases of true SIBO (detecting only around 60% of cases).[vii] Nevertheless, a clear positive result can provide useful information.

In most locations, you can order a SIBO breath test yourself online. Testing options include:

United States

United Kingdom


Food allergy & sensitivity testing

There are two types of antibodies that can drive reactions to foods. IgE antibodies are responsible for true food allergies, while IgG antibodies can cause “sensitivites”, with more subtle reactions and perhaps a more signficant time lag before symptoms appear.  Regulary eating a food that you react to with either type of antibody can potentially exacerbate inflammation in the skin or joints.

Testing for IgE antibodies is typically done through a doctor’s order at standard laboratories, such as LabCorp or Quest. However these tests often have only a short number of foods included in each panel.  (Skin prick testing through an allergist is another option).

Most allergists do not recognize IgG sensitivity testing as valid. Yet studies have found that eliminating foods that arthritis patients react to with IgG antibodies can reduce the severity of joint pain and swelling.  One of the most popular options for IgG food sensitivity testing is the Cyrex Array 10 Multiple Food Immune Reactivity Panel.  This is quite expensive, but can be ordered without a doctor’s assistance here.

A less expensive option is available through Life Extension. In addition to being lower cost, this test requires only blood spots on a card, rather than a blood draw, so is less hassle. Nevertheless, it is likely to be less sensitive.

A final alternative is the Dunwoody Dietary Antigen Complete Panel. This tests for both IgE and IgG antibodies to a wide variety of foods.  (I do not know enough about the company to outright recommend it, but this is the test that appeared to be the most useful and accurate in my particular case.) It can be ordered in the US here and in the UK here.

To get the most value from IgG testing, it is important to eat a wide variety of foods for several weeks leading up to the test.  The test will only report positive results for foods that have been eaten relatively recently.



[i] Viladomiu, M., Kivolowitz, C., Abdulhamid, A., Dogan, B., Victorio, D., Castellanos, J. G., … & Chai, C. (2017). IgA-coated E. coli enriched in Crohn’s disease spondyloarthritis promote TH17-dependent inflammation. Science Translational Medicine, 9(376), eaaf9655;

Ramírez-Boscá, A., Navarro-López, V., Martínez-Andrés, A., Such, J., Francés, R., de la Parte, J. H., & Asín-Llorca, M. (2015). Identification of bacterial DNA in the peripheral blood of patients with active psoriasis. JAMA dermatology, 151(6), 670-671

Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., … Littman, D. R. (2013). Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife, 2, e01202.

Maeda, Y., Kurakawa, T., Umemoto, E., Motooka, D., Ito, Y., Gotoh, K., … & Sakaguchi, N. (2016). Dysbiosis contributes to arthritis development via activation of autoreactive T cells in the intestine. Arthritis & Rheumatology, 68(11), 2646-2661.

Chen, J., Wright, K., Davis, J. M., Jeraldo, P., Marietta, E. V., Murray, J., … & Taneja, V. (2016). An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome medicine, 8(1), 43.

[ii] Ojetti, V., De Simone, C., Aguilar Sanchez, J., Capizzi, R., Migneco, A., Guerriero, C., … & Gasbarrini, A. (2006). Malabsorption in psoriatic patients: cause or consequence?. Scandinavian journal of gastroenterology, 41(11), 1267-1271.

Peslyak, M., Gumayunova, N., Nesterov, A., & Potaturkina-Nesterova, N. (2012). Small intestine microflora at psoriasis. Its possible role in pathogenesis. In 3rd World Psoriasis & Psoriatic Arthritis Conference.

Drago, F., Ciccarese, G., Indemini, E., Savarino, V., & Parodi, A. (2017). Psoriasis and small intestine bacterial overgrowth. International journal of dermatology.

[iii] Henriksson, A. E., Blomquist, L., Nord, C. E., Midtvedt, T., & Uribe, A. (1993). Small intestinal bacterial overgrowth in patients with rheumatoid arthritis. Annals of the rheumatic diseases, 52(7), 503.

[iv] Pimentel, M., Wallace, D., Hallegua, D., Chow, E., Kong, Y., Park, S., & Lin, H. C. (2004). A link between irritable bowel syndrome and fibromyalgia may be related to findings on lactulose breath testing. Annals of the rheumatic diseases, 63(4), 450-452.

[v] Drago, F., Ciccarese, G., Indemini, E., Savarino, V., & Parodi, A. (2018). Psoriasis and small intestine bacterial overgrowth. International journal of dermatology, 57(1), 112-113.

[vi] Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112;

Pimentel, M., Chow, E. J., & Lin, H. C. (2000). Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. The American journal of gastroenterology, 95(12), 3503-3506.

[vii] Drago, F., Ciccarese, G., Indemini, E., Savarino, V., & Parodi, A. (2018). Psoriasis and small intestine bacterial overgrowth. International journal of dermatology, 57(1), 112-113.