How to Test for IBS Root Causes
IBS and its common symptoms like constipation and diarrhea always have a root cause. The challenge is that many of these root causes share similar symptoms. So how do we find what's causing a client's IBS symptoms? Our motto is "test, don't guess." Functional root cause IBS testing has helped thousands of our clients move beyond an 'IBS' label to actually identify why they have symptoms and take effective action to address them.
Because of the recent advances in gut health research and testing, many of these root causes (like SIBO, gut infections and leaky gut) might not be on the radar of your local doctor… or not yet, anyway. And while you may have had basic testing previously, diagnostics around gut health have been evolving rapidly over the last few years, as have clinical interpretations.
After experiencing a downward health spiral that left me with gut symptoms, weight gain, fatigue, and bad skin despite eating a basic, unprocessed diet, I finally found answers through functional health tests. These tests changed my life, and I wish I had known about them earlier when I was first diagnosed with IBS.
So, with that in mind, here is a summary of what we are going to cover:
Why you need to test, not guess when it comes to IBS
Common tests for IBS root causes and when we consider using them
A basic overview of how to do each test
Example test results for each lab
Some key markers we look for; and
The one test we order for almost every one of our clients.
Why do I need IBS testing?
Many of the root causes of IBS have multiple overlapping symptoms. Which is part of the reason they've been lumped together under a single term "IBS" (Irritable Bowel Syndrome) for so long. To address each of these root causes effectively, you need a targeted protocol specific to each imbalance. There's no one-size-fits-all solution for IBS, which is why clinical trials looking for a universal ‘cure’ always fail. Different issues require different interventions.
That's why it's so important to "test, don't guess" when it comes to IBS root causes. While there are many different tests available for more complex cases, here are my five go-to IBS tests that address the most common root causes of IBS that we see at The Functional Gut Health Clinic.
Functional Labs: IBS Testing for Root Causes
1. GI Map Stool Test
The GI Map Stool Test is a comprehensive DNA stool test that uses PCR technology to identify gut infections and microbiome imbalances. It’s our go-to test for many IBS clients.
What does a GI Map Test for?
There are a whole range of markers on a stool test like the GI Map that help us get a really clear idea about what is going on inside your large intestine that may be contributing to your IBS symptoms. A stool test also gives us clues about other parts of the digestive system, like the stomach, small intestine, liver, gall-bladder and pancreas.
This is why I like my clients to start with a simple one-day sample stool test that they can do at home. But most importantly, a stool test gives us information about whether you have a dysbiosis - imbalance of good, bad and commensal bacteria in the large intestine, and/or a gut infection such as those caused by parasites, bacteria, viruses, worms and yeast/fungus.
What Are the Key Markers on a GI Map and What Do They Mean?
There are three broad categories of markers that we look at on a GI Map to identify healing opportunities for IBS. These are pathogenic species, beneficial gut flora, and intestinal health markers.
Pathogenic species: Whether these are identified in 'high' numbers or are simply 'detectable', pathogenic species are almost always something we need to address. These include gut infections like parasites, worms and H. pylori, viruses, pathogenic and opportunistic bacteria, yeast/fungus.
Beneficial gut flora: This section gives us clues about the overall abundance and diversity of your 'good' gut bacteria and whether there is a dysbiosis - an imbalance of good, bad and commensal bacteria in the large intestine.
Intestinal health markers: These provide information about digestive function, inflammation, immune function, and a helpful 'leaky gut' marker (zonulin).
Example GI Map Test Result (2 page extract)
There are a whole range of markers on a stool test that help us get a really clear idea about what is going on inside your large intestine that may be contributing to your IBS symptoms. But a stool test also gives us clues about other parts of the digestive system, like the stomach, small intestine, liver, gall-bladder and pancreas. This is why I like my clients to start with a simple one-day sample stool test, that they can do at home. But most importantly, a stool test gives us information about whether you have a dysbiosis - imbalance of good, bad and commensal bacteria in the large intestine, and/or a gut infection such as those caused by parasites, bacteria, viruses, worms and yeast/fungus.
The GI Map by Diagnostic Solutions Laboratory (or Complete Microbiome Mapping as it is called in Australia), is the latest evolution of comprehensive DNA stool testing, using PCR technology. Before this testing was available locally in Australia, I would use a GI Map on many of my IBS clients whose symptoms remained despite a 'clean' CDSA stool test (see #1B below) and I was amazed at the number of pathogens and elevated markers that showed up on the GI Map to further inform our healing approach.
What are the key markers and what do they mean?
There are three broad categories of markers that we look at on a GI Map to identify healing opportunities for IBS. These are pathogenic species, beneficial gut flora and intestinal health markers.
> Pathogenic species: whether these are identified in 'high' numbers or are simply 'detectable', pathogenic species are almost always something we need to address. These include parasites, worms, H. pylori, viruses, pathogenic and opportunistic bacteria, yeast/fungus.
> Beneficial gut flora: this section gives us clues about the overall abundance and diversity of your 'good' gut bacteria (microbiome).
> Intestinal health markers: these provide information about 'digestive fire', inflammation, your immune function and a helpful 'leaky gut' marker (zonulin).
Example GI Map Test Result (2 page extract)
2. SIBO Breath Test
If bloating, gas, abdominal pain, or irregular bowel movements are part of your daily life, especially if they improve temporarily with antibiotics or worsen with high-fiber foods, the root cause might be SIBO, or Small Intestinal Bacterial Overgrowth. Researchers think that up to 80% of diagnosed IBS cases might actually be SIBO. We use a SIBO breath test to identify whether there is a bacterial or archaea overgrowth in the small intestine.
What will a SIBO Test tell you?
SIBO is an overgrowth of bacteria or archaea in the small intestine. The way we test for this is with a breath test. You drink a sugar solution (lactulose, glucose or fructose), let the microbes ferment the sugar, which creates gas (hydrogen, methane or hydrogen sulfide), and then we measure that gas in your breath every 15-20 minutes over a three hour period. The amount of gas and the timing of its elevation during that period give us a lot of information about what is happening in your small intestine.
What Are the Key Markers on a SIBO Breath Test and What Do They Mean?
When looking at a SIBO breath test, we use a combination of the North American Consensus Guidelines as well as a client's health history, symptoms and our own clinical experience with thousands of SIBO clients. Here are the key measurements:
Hydrogen Positive SIBO:
North American Consensus: A rise of 20ppm in hydrogen above baseline within 90 minutes.
Our Clinical Adaptation: Hydrogen levels of 20ppm or higher within 90-100 minutes, and up to 120 minutes for constipated clients with slower transit times.
Methane Positive SIBO:
North American Consensus: Methane levels of 10ppm at any point during testing, including baseline.
Our Clinical Adaptation: Methane levels of 10ppm or higher at any point during testing, including baseline. We may also consider methane positive when levels are between 3-9ppm for clients with chronic constipation and no other clues to explain their symptoms. Remember, symptom severity doesn’t always correlate with gas levels—clients with low gas levels can still have severe symptoms.
Hydrogen-Sulfide Positive SIBO:
While hydrogen sulfide is not addressed in the North American Consensus, our clinical adaptation considers hydrogen sulfide positive as:
3ppm or higher within 90-100 minutes on a lab that measures hydrogen sulfide gas, and up to 120 minutes for constipated clients with slower transit times.
A flatline of both hydrogen and methane gas levels on a breath test where H2S gas isn’t measured. We want to see hydrogen of 4-6ppm or below and methane of 3ppm or below for the whole 3-hour testing period to be considered a flatline. The theory is that hydrogen sulfide-producing bacteria consume all the hydrogen made by bacteria (used by archaea to make methane) and convert it to hydrogen sulfide gas, resulting in a flatline on the hydrogen-methane report.
Example SIBO Breath Test ResultS
3. DUTCH Hormone Test
If in addition to IBS symptoms, you’re also experiencing fatigue, mood changes, unexplained weight shifts, or if digestive issues coincide with hormonal fluctuations, it's time to check in on your hormones. Hormonal imbalances can directly impact gut health by affecting gut motility, microbiome composition, and the integrity of the gut lining. The most comprehensive hormone panel we use is the DUTCH Complete Test.
What will a DUTCH Test tell you?
The DUTCH (Dried Urine Test for Comprehensive Hormones) Test provides a detailed overview of your body’s hormonal landscape, including sex hormones and adrenal hormones, and insights into metabolic pathways and nutritional markers.
What Are the Key Markers and What Do They Mean?
Sex Hormones: Estradiol, Progesterone, and Testosterone: These hormones are critical for reproductive health and can influence mood, energy levels, and overall well-being. Imbalances in these hormones can also affect gut health and contribute to IBS symptoms.
Adrenal Hormones: DHEA and Cortisol. These hormones play a significant role in the body's stress response. Cortisol, for example, can affect gut microbes by altering gut transit time, increasing leaky gut, and reducing nutrient availability. Elevated cortisol levels due to chronic stress can exacerbate IBS symptoms.
Metabolic Pathways and Nutritional Markers:
Liver Function Indicators: The DUTCH test provides insights into how well your body is metabolizing and detoxifying hormones, which can impact overall health and gut function.
Estrogen Metabolism: The percentage of estrogen flowing down the 16-OH pathway can indicate gut dysfunction and inflammation.
B Vitamins and Glutathione needs: The DUTCH test includes nutritional organic acid markers that give clues about vitamin deficiencies and oxidative stress levels, which can impact gut health and overall well-being.
DUTCH Test Collection Process:
For cycling females, the test needs to be done during the luteal phase of the cycle. For everyone else, it can be done at any time during the month. The test involves collecting four to five dried urine samples over a 24-hour period.
Example DUTCH Test Result (2 page EXTRACT)
4. Organic Acids Test (OAT)
The OAT is particularly relevant if, along with IBS symptoms, you’re also dealing with systemic symptoms like fatigue, mood changes, and brain fog. It helps us identify additional root causes that may have been missed with stool and SIBO testing.
What will an OAT test tell you?
This test looks at metabolic byproducts in urine to assess factors like mold colonization, yeast and bacteria, mitochondrial function, neurotransmitters, detoxification, and nutritional status. The OAT provides additional insights into potential root causes, allowing us to refine and tailor our protocol recommendations.
What Are the Key Markers and What Do They Mean?
The OAT provides a comprehensive overview of several critical areas related to gut health and overall well-being:
Yeast and Fungal Markers: Indicators of overgrowths that can affect gut health and contribute to symptoms like brain fog and fatigue.
Bacterial Markers: Clues about bacterial overgrowths or imbalances that may not have been detected by stool testing.
Oxalate Metabolites: These markers can be helpful for clients with pain symptoms related to mold or yeast, as well as genetic reasons for elevated oxalates.
Mitochondrial Function: Assessments of how well your cells are producing energy, which can impact overall energy levels and fatigue.
Neurotransmitter Metabolites: Insights into how well your body is producing and breaking down neurotransmitters, which can affect mood and mental health.
Detoxification Indicators: Markers that show how well your body is detoxifying harmful substances, including mycotoxins from mold.
Nutritional Status: Information about nutrient deficiencies that could be impacting your gut health and overall wellness.
Example OAT Test Report (2 page extract)
5. Mycotoxin Testing
Our number one blocking factor to addressing the most common IBS root causes is mold and mycotoxins, which are actually IBS root causes themselves. Mold and the toxic compounds produced by certain types of molds, called mycotoxins, can significantly impact health across many areas of the body, including the digestive system. If you've been working on your gut health for years and had extensive exposure to a water-damaged building, mold and mycotoxins might be the missing piece of the puzzle. Mycotoxins can contribute to a wide range of symptoms, including chronic fatigue, sinus issues, brain fog, pain, light sensitivity, headaches, and mood changes.
What will a Mycotoxin test tell you?
Mycotoxin testing assesses your body’s exposure to mold by measuring mycotoxin levels in urine. The test involves a simple first-morning urine sample that assesses mycotoxin levels produced by mold fungi. Most tests screen for eleven or more different mycotoxins from various species of mold.
What Are the Key Markers and What Do They Mean?
These test reports, as you’ll see below, are pretty basic and are just showing on a simple scale, the level of exposure to specific mycotoxins. We are looking to see if mycotoxins like Ochratoxin, Gliotoxin, and Mycophenolic acid show as elevated in the report. These toxic compounds can trigger inflammation and immune reactions, exacerbating GI symptoms and impacting overall health.
While advanced tests like mycotoxin testing offer incredible insights into your health, it's essential to use them alongside a thorough health history and clinical correlation. Testing provides clues that help create a comprehensive understanding of your health.
Example MycoTOX Profile Report (2 page extract)
What IBS Testing Do I Need?
Choosing the right test depends on your symptoms and health history. In our clinic, we often start with a comprehensive stool test like the GI Map and, where indicated, a SIBO breath test. These foundational labs provide a great starting point for identifying and addressing imbalances that lead to IBS symptoms.
Because testing can be expensive, it's not always necessary to do all the tests. We actually find that too much information at the beginning can be overwhelming for clients. Usually, a GI Map or SIBO Breath Test reveals enough imbalances for clients to address to begin making significant improvements with symptoms.
Work with our team
If you're ready to move past an IBS label and uncover the root causes of your symptoms, our team of functional nutritionists can help. We specialize in root cause testing and natural protocols for IBS, providing personalized guidance and support every step of the way. Visit our Work With Us page to learn more about how we can help you take control of your gut health and start your journey to feeling healthy, vibrant, and well.