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Top Gut Secrets: How to Test for Dysbiosis, SIBO, and Leaky Gut

Your internal ecology has everything to do with your health. It is stunning to me that the gut is so smart and complex, yet so vulnerable. I’m sure you won’t be surprised to learn that many lifestyle factors directly impact your gut barrier and can lead to leaky gut, including eating certain foods, drinking too much alcohol, skimping on fiber, not sleeping enough, and wayward hormones such as cortisol and melatonin. After all, the gut wall is made up of thumbs-up-gutonly a single layer of tiny cells, which allow in nutrients and water while keeping out bacteria, large proteins, and other toxins. You can think of the gut wall as the bouncer of the club of your body, giving access only to those worthy of entry while blocking the entrance to the bad guys. But you must remember that the bouncer is more vulnerable than you may realize. When the gut wall develops tiny holes in it, it’s as if the bouncer has left the door unattended plus opened several other entrances, allowing bad guys to flood in and wreak havoc. Considering that the gut wall is only a thin layer of cells, it’s easy to imagine how toxins often sneak past it and find their way in to the rest of you body. This is precisely what happens when you have a leaky gut: unwanted toxins crash your party, trash your immune system, and the body shuts down with inflammation. As a result, you get fat, cranky, tired, and bloated. The scientific name for leaky gut syndrome is intestinal hyperpermeability. What are the most common causes of leaky gut, or increased intestinal permeability?
  1. Antibiotic use and abuse
  2. Low gastric acid production
  3. Dysbiosis (see below for four types)
  4. NSAID use (such as ibuprofen)
  5. Excess stress
  6. Alcohol both increases intestinal permeability and feeds pathogenic bacteria
  7. Eating allergenic foods such as gluten and dairy
  8. Low secretory IgA (SIgA, see stool test below for further details)
Dysbiosis is one of the key triggers for leaky gut, and there are four types. [1] You can have more than one type at a time. Here they are:
  1. Loss of good bacteria, also known as keystone taxa;
  2. Loss of microbial diversity;
  3. Shifts in metabolic capacity, usually a result of growing more bad bacteria that harvest excess energy from food;
  4. Blooms of pathogens, such as yeast overgrowth or parasites.
If you want to fix dysbiosis, most of the time you need to remove bad bugs, such as bacteria, parasites, or excess yeast. In fact, you need to employ the full 5Rs: Remove, Replace, Reinoculate, Repair, Rebalance. But before I get ahead of myself, we should talk through the testing for dysbiosis and leaky gut. It’s important to understand that dysbiosis is not detected by routine tests that your conventional doctor may order. That’s why it’s important to be aware of the type of testing that’s available to you, so that you can see if your gut is causing symptoms for you.

Testing, Testing, Testing

You can test for leaky gut and dysbiosis, but as with most medical tests, the results aren’t perfect. That’s why I recommend that you work with a wise clinician who can provide accurate synthesis. There isn’t one single test that definitively confirms dysbiosis; rather, you need a collaborative, experienced guide who can provide a gestalt from your story, symptoms, and tests. That said, here are a few tests to consider. Keep in mind that I do not work with children, so my comments apply only to adults.
  1. Hydrogen breath test. This test measures how much hydrogen you exhale after consuming a sugar-based solution and breathing into a balloon-like container or test tube. It’s used to assess for small intestinal bacterial overgrowth (SIBO), [2] fructose intolerance, and/or lactose intolerance. In conventional medicine, the breast test is often used in inflammatory bowel disease and other functional gastrointestinal disorders. [3] For the hydrogen breath test, you drink a solution that contains lactulose, which can be fermented by small intestine bacteria. You collect expelled air after drinking the sugar solution into a little tube, and then you send that tube to the lab, which tests it for specific gases that are produced by different kinds of bacteria.  If the levels of the certain gases are high, then that suggest you may have small intestinal bacterial overgrowth. Now for the bad news: for accurate test results, you must avoid certain foods, drinks, supplements, and medicines before the test.Check your lab for details, but that usually means no probiotics for 5 days prior to the test, and avoiding vegetables, fruit, and alcohol the day before the test. Several gastroenterologists and other experts offer the test in their office, which is what I recommend, or you can perform a home test by Commonwealth Labs ($300) or Metabolic Solutions ($125). If you have experience with this test, let us know in the comments section below or on Facebook, as we have found in my practice that the home testing may be less reliable.
  1. Organic acids test. Performed on the urine by labs such as Genova Diagnostics and Great Plains Lab. Organic acids are byproducts of microbial metabolism so they provide a metabolic snapshot of what’s happening in your body. When increased in the urine, they may suggest an overgrowth of certain bacteria and/or yeast.  Organic acids may also provide data on important neurotransmitters, nutritional markers, glutathione status, oxalate metabolism, and more. They usually cost about $300 and up.

Here are a few examples:

Arabinose and tartaric acid are produced by Candida. When your levels are high, this can suggest yeast overgrowth

Excess DHPPA (dihydroxyphenylpropionic acid) indicates intake of chlorogenic acid, a common substance in beverages, many fruits, and vegetables. Harmless or benecial bacteria such as Lactobacilli, Bifidobacteria, and E. coli increase the breakdown of chlorogenic acid to DHPPA, so high values are associated with increased amounts of these species in the gut.

  1. Leaky gut tests. These are rarely used any more, but the goal is to assess small intestinal absorption and barrier function in the bowel. As you know, the small intestine functions as a digestive/absorptive organ for nutrients as well as a powerful immune and mechanical barrier against excessive absorption of bacteria, food antigens, and other macromolecules. Both malabsorption (decreased permeability) and leaky gut (increased intestinal permeability) are associated with chronic gastrointestinal imbalances as well as many systemic disorders. You measure the ability of two non-metabolized sugar molecules to permeate the intestinal mucosa by drinking a premeasured amount of lactulose and mannitol. Again, Genova offers a test that I have ordered on patients in the past if I was unsure about their diagnosis or needed additional objective information.
  1. Stool tests. A stool analysis can be done to identify your mix of microbes, from good bacteria to bad bacteria, yeast overgrowth, and parasites. A few points to keep in mind:

Look for a test that provides identification of pathogenic species and susceptibility testing so that you and your clinician can choose the most appropriate pharmaceutical or natural treatment agents.

One of the important markers to measure is beta glucuronidase, which is an important enzyme involved in breaking down estrogen so it doesn’t keep circulating in the body like bad karma.

Another key marker is secretory immunoglobulin A (SIgA) a biomarker that functional medicine clinicians track to assess for adrenal dysregulation and decreased immune function. SIgA is the main immune defense of your gastrointestinal tract against foreign bacteria, parasites, viruses, and yeast. It can be measured in your blood and stool. low SIgA makes you more likely to have infections and other problems in your gut.

Most stool tests are pricey at around $500 and up, such as by Doctor’s Data and Genova, but you can also map your microbiota with ubiome, a citizen scientist group designed to crowd source information on the gut flora. Ubiome starts at $89 but it does not include susceptibility testing, beta-glucuronidase, SIgA, or other functional tests.


There are many ways to prevent and/or reverse leaky gut, dysbiosis, and autoimmunity. In functional medicine, that means identifying the root cause, particularly the food and lifestyle triggers. Then you swap nutrient-dense and healing foods for the toxic foods, and do the same with lifestyle redesign. I’ve got to be honest with you; the process of healing the gut is rarely fast or easy. It’s not as simple as cutting out gluten, adding a forkful of sauerkraut, and popping a few betaine HCl supplements. Leaky gut and dysbiosis are serious problems that deserve your attention—many people have it but don’t know it. To learn more about whether you have a problem with your gut and how to heal it, join my upcoming free webinar right here. We will make it as easy to understand the complex science, plus offer several proven solutions!   [1] http://www.ncbi.nlm.nih.gov/pubmed/25974298 [2] http://www.ncbi.nlm.nih.gov/pubmed/24095975 [3] http://www.ncbi.nlm.nih.gov/pubmed/25523187; http://www.ncbi.nlm.nih.gov/pubmed/25298621  


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