Dysbiosis Symptoms, Testing, & Treatment

Test tubes used to test digestive function

As digestive issues are a main clinical focus area of mine, I spend many hours a week endeavouring to keep up with the latest research. Chronic digestive cases are downright complicated, for both the patient and often the practitioner. And because the gut is at the centre of a patient’s health — as Hippocrates so eloquently put it, “All disease begins in the gut” — we are seeing accumulating evidence that the origin of other diseases may lie in the gut as well. Cue Parkinson’s disease, autoimmune diseases, anxiety and depression … Need I continue? A healthy gut microbiome is truly crucial for one’s overall health.

There are several gut tests available, none of which provide a black-and-white answer to diagnosing dysbiosis. However, the utility of these tests are that they provide us with clues about the function and machinery of the gastrointestinal tract, which helps inform treatment direction and additional testing.

In irritable bowel syndrome (IBS), dysbiosis is a primary driver that is implicated in this conditions. There is strong evidence of a relationship between modifications to the composition of gut microbiota and the development of IBS — specifically, where the healthy balance of gut microorganims becomes disrupted, causing chronic, persistent dysbiosis and a host of gastrointestinal symptoms.[1]

Signs and symptoms of gut dysbiosis

The signs and symptoms of gut dysbiosis are essentially the “classic” IBS picture. They can include any or all of the following:

  • Abdominal discomfort or indigestion that worsens after eating

  • Bloating and/or distention

  • Abdominal pain

  • Excessive gas

  • Inconsistent bowel movement patterns — e.g. diarrhea, constipation, or mixed patterns

  • Acid reflux

  • Rectal itching

Diagnosis of gastrointestinal disease is conventionally done by using pictures — in particular, endoscopies, colonoscopies, scans, and biopsies. These tests are paramount for diagnosing cancer, inflammatory bowel disease, diverticulitis, and other anatomical abnormalities, but are not particularly useful for those who suffer from “functional gastrointestinal disorders” such as IBS.

While there is no perfect test, the tests outlined below can help rule in (or out) dysbiosis and provide clues as to the location of the problem.

Ova & Parasite Stool Test

This test determines whether a parasite is infecting the gastrointestinal tract, causing symptoms such as diarrhea. A wide variety of parasites can infect humans. These include Giardia, Cryptosporidium (or “crypto), Entamoeba histolytica, and Blastocystis hominis.

Blastocystis hominis (B. hominis) is of particular interest to those who have IBS. While it commonly lives in the digestive tract as a commensal parasite without causing harm, an association between IBS and B. hominis has been suggested in the literature.[2,3] B. hominis seems to be a marker of intestinal dysfunction in those who have IBS, rather than a cause of IBS.[3] For many individuals who have IBS and a B. hominis overgrowth, we see hallmark symptoms of dysbiosis like bloating, diarrhea, weight loss, and abdominal pain.

Comprehensive Digestive Stool Analysis (CDSA)

This test looks specifically at the large intestine, and can be useful for individuals who have IBS, malabsorption, inflammatory bowel disease, and the above-mentioned symptoms of dysbiosis. It includes bio-markers and markers of inflammation which offer valuable insight into overall gut health, some of which are described below:

  • Short chain fatty acids (SCFA). These are the main metabolites produced in the gastrointestinal tract by bacterial fermentation of dietary fibre. It is thought that short chain fatty acids play a key role in gut-brain communication.[4] Short chain fatty acids are the main source of nutrition for the cells in the colon. A higher intake of dietary plants is associated with increased SCFAs in stool.[5]

  • Secretory IgA. The role of secretory IgA is to protect the surface of the gut against viruses, bacteria, parasites, and toxins. Many people with chronic digestive issues have low levels of secretory IgA. Interestingly, B. hominis (as described above) has been shown to deactivate human secretory IgA.[6] Low levels of secretory IgA are, in fact, associated with carrying this parasite.[7]

  • Beta-glucuronidase. Beta-glucuronidase is a bacterial enzyme located in the large bowel that plays a role in how much estrogen in is in the body. This enzyme’s job is to deconjugate estrogen. When estrogen becomes deconjugated, it is able to become reabsorbed by the large bowel and re-enter circulation. This is where our digestive health meets hormonal conditions: too little beta-glucuronidase can be related to hypo-estrogenic conditions like metabolic syndrome, cardiovascular disease and cognitive decline, whereas too much beta-glucuronidase can be related to estrogen dominant conditions like endometriosis and breast cancer.[8]

  • Fecal calprotectin. Fecal calprotectin is a reliable marker of inflammation in the gut and is useful for differentiating between inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS).[9]

  • Elastase. Elastase levels provide information on how well the pancreas is working. Correlations between low levels of elastase and chronic pancreatitis have been reported.[10] When elastase levels are low, we would expect increased levels of vegetable or protein fibres or elevated fat levels in the stool.

  • Yeast culture. The quantity of yeast found in the stool sample is provided and may be helpful in identifying potential yeast overgrowth.

  • Muscle fibres, carbohydrates, and fat stain. Muscles fibres in the stool are an indicator of incomplete digestion. Similarly, high fecal fat levels and carbohydrate levels may indicate fat and carbohydrate malabsorption. Fat malabsorption has been seen in cases of small intestinal bacterial overgrowth (SIBO), as the bacteria in the small intestine is able to deconjugate bile salts.[11]

  • White blood cells and mucous. White blood cells and mucous in the stool can occur with bacterial and parasitic infections. They may also be seen with with irritation to the bowel mucosal surface and in inflammatory bowel diseases such as Crohn’s disease or ulcerative colitis.

Small Intestinal Bacterial Overgrowth (SIBO) Breath Test

Small intestinal bacterial overgrowth (SIBO) is the abnormal overgrowth of bacteria in the small intestine that leads to several digestive symptoms, including bloating, abdominal pain and cramps, constipation, diarrhea, heartburn, nausea, food sensitivities, etc. This test measures abnormal levels of hydrogen and methane found in the breath that are produced if there is malabsorption of carbohydrates and/or bacterial overgrowth in the small intestine.

One of the many challenges I have with this test is its significant degree of false positives and false negatives. As a practitioner, I am not entirely confident in the test results, and may proceed with treatment of SIBO without testing. In Canada, the drug Rifaxamin (which is out of the scope of Naturopathic Doctors) was approved in 2018 by Health Canada for the treatment of IBS-D and is also the gold standard treatment for SIBO.

It’s important to understand that not all IBS is caused by SIBO; in fact, recent data shows that the percentage of IBS sufferers who have SIBO is grossly overestimated. There are, however, some factors that would make someone more likely to have SIBO. These include: long-term use of PPI medication, poorly controlled diabetes resulting in gastroparesis, motility disorders of the gut, and a bowel resection.

Candida

Candida is the most common cause of fungal infection in humans. Candida is a yeast that lives at low levels in the healthy human gut; however, when it overgrows, it can lead to a range of symptoms including bloating and gas, chronic sinusitis, fatigue, genitourinary infections like vaginal yeast infections, brain fog, and a white coating on the tongue.

Candida can be measured in the stool and in the blood. The above Comprehensive Digestive Stool Analysis test includes the microscopic examination as well as culture of yeast in the stool. In blood, candida antibodies and antigen are measured.

Blood tests

There are no direct markers in the blood that will show whether an individual has intestinal dysbiosis. However, dysbiosis is often accompanied by greater intestinal permeability and impaired nutrient absorption. Individuals who have SIBO or Blastocystis hominis may be more likely to have vitamin deficiencies, namely iron, vitamin B12, and fat-soluble vitamins like vitamins A, D, E, and K.[12] Blood tests can be used to determine whether vitamin/nutrient deficiencies are occurring concurrently with dysbiosis.

Blood tests are also important to evaluate inflammatory markers, specifically erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP). These levels are typically not elevated in patients who have IBS or SIBO, but are typically elevated in those who have Crohn’s and colitis.

Treatment

Treating dybiosis is highly individualized. It depends on the test results, blood labs, symptoms, and history preceding the onset of symptoms. Below are treatment fundamentals that may be helpful in keeping dysbiosis and accompanying digestive symptoms at bay.

  1. Diet. Studies have shown that a low-FODMAP diet improves IBS symptoms — specifically abdominal pain, bloating, constipation, diarrhea, abdominal distention, and gas.[13] While this diet is somewhat restrictive and does not address the root cause of dysbiosis, it can help improve symptoms and quality of life.

  2. Exercise. Exercise positively modifies our gut bacteria by promoting a more diverse microbiome and enhancing the number of beneficial microbial species.[14] Regular exercise is an excellent way to support a healthy gut.

  3. Bone broths. Bone broths are a source of gelatin, glutamine, and minerals. Gelatin and glutamine provide amino acids that promote gut healing, which is important in heightened intestinal permeability as seen in IBS and IBD. L-glutamine has also been found to reduce inflammation in both IBS and IBD patients.[15, 16]

  4. Keep the bowels moving. This is especially pertinent for those who are constipation prone. Many patients will report that their bloating and gas worsens when they are extra constipated. Natural osmotic laxatives such as magnesium citrate or vitamin C can help promote quicker stool transit time.

  5. Mindfulness and meditation. Many people find this challenging, but it plays a significant role in helping reduce gastrointestinal symptoms. 15 to 20 minutes of meditation per day has been studied in both IBS and IBD to improve disease-related symptoms, anxiety, and overall quality of life.[17]

If you have chronic digestive issues, working with a primary care provider such as your naturopathic doctor or family physician (preferably both) is imperative. While IBS is a diagnosis of exclusion, it is also often a misdiagnosis, where symptoms can be due to a more serious underlying cause. Receiving the right guidance and medical advice is of utmost importance on your gut-healing journey.

- Dr. Dominique Vanier is a registered naturopath in Burlington with a clinical focus on digestion and women’s hormones. Naturopath Burlington. This article is for information purposes only. It is not intended to treat or diagnose any health conditions.

References

[1] Principi, N., Cozzali, R., Farinelli, E., Brusaferro, A., & Esposito, S. (2018). Gut dysbiosis and irritable bowel syndrome: The potential role of probiotics. Journal Of Infection, 76(2), 111-120. doi: 10.1016/j.jinf.2017.12.013

[2] Ragavan, N., Kumar, S., Chye, T., Mahadeva, S., & Shiaw-Hooi, H. (2015). Blastocystis sp. in Irritable Bowel Syndrome (IBS) - Detection in Stool Aspirates during Colonoscopy. PLOS ONE, 10(9), e0121173. doi: 10.1371/journal.pone.0121173

[3] Coyle, C., Varughese, J., Weiss, L., & Tanowitz, H. (2011). Blastocystis: To Treat or Not to Treat... Clinical Infectious Diseases, 54(1), 105-110. doi: 10.1093/cid/cir810

[4] Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in microbiota–gut–brain communication. Nature Reviews Gastroenterology & Hepatology. doi: 10.1038/s41575-019-0157-3

[5] De Filippis F, Pellegrini N, Vannini L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65:1812-1821.

[6] Poirier, P., Wawrzyniak, I., Vivarès, C., Delbac, F., & El Alaoui, H. (2012). New Insights into Blastocystis spp.: A Potential Link with Irritable Bowel Syndrome. Plos Pathogens, 8(3), e1002545. doi: 10.1371/journal.ppat.1002545

[7] Nagel, R., Traub, R. J., Kwan, M. M., & Bielefeldt-Ohmann, H. (2015). Blastocystis specific serum immunoglobulin in patients with irritable bowel syndrome (IBS) versus healthy controls. Parasites & vectors, 8, 453. doi:10.1186/s13071-015-1069-x

[8] Baker, J., Al-Nakkash, L., & Herbst-Kralovetz, M. (2017). Estrogen–gut microbiome axis: Physiological and clinical implications. Maturitas, 103, 45-53. doi: 10.1016/j.maturitas.2017.06.025

[9] D'Angelo, F., Felley, C., & Frossard, J. (2017). Calprotectin in Daily Practice: Where Do We Stand in 2017?. Digestion, 95(4), 293-301. doi: 10.1159/000476062

[10] Nandhakumar, N., & Green, M. (2010). Interpretations: How to use faecal elastase testing. Archives Of Disease In Childhood - Education And Practice, 95(4), 119-123. doi: 10.1136/adc.2009.174359

[11] Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122.

[12] Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122.

[13] Nanayakkara, W. S., Skidmore, P. M., O'Brien, L., Wilkinson, T. J., & Gearry, R. B. (2016). Efficacy of the low FODMAP diet for treating irritable bowel syndrome: the evidence to date. Clinical and experimental gastroenterology, 9, 131–142. doi:10.2147/CEG.S86798

[14] Mailing, L., Allen, J., Buford, T., Fields, C., & Woods, J. (2019). Exercise and the Gut Microbiome. Exercise And Sport Sciences Reviews, 47(2), 75-85. doi: 10.1249/jes.0000000000000183

[15] Kim, M. H., & Kim, H. (2017). The Roles of Glutamine in the Intestine and Its Implication in Intestinal Diseases. International journal of molecular sciences, 18(5), 1051. doi:10.3390/ijms18051051

[16] Zhou, Q., Verne, M., Lefante, J., Basra, S., Salameh, H., & Verne, G. (2018). Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut, 68(6), 996-1002. doi: 10.1136/gutjnl-2017-315136

[17] Kuo, B., Bhasin, M., Jacquart, J., Scult, M., Slipp, L., & Riklin, E. et al. (2015). Genomic and Clinical Effects Associated with a Relaxation Response Mind-Body Intervention in Patients with Irritable Bowel Syndrome and Inflammatory Bowel Disease. PLOS ONE, 10(4), e0123861. doi: 10.1371/journal.pone.0123861