Common errors practitioners make addressing gut microbiome imbalances

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By Carolina Brooks, BA, IFMCP

Many clinicians are starting to offer more integrative approaches to their patients. The biggest challenge I believe many practitioners face is learning to navigate the complex protocols taught by experts, companies, and leaders in the field with their own thought processes, as well as building confidence to apply these concepts to an individual patient—with their unique health history, drivers, triggers, and mediators—in a way that will allow them to heal and improve in a progressive manner.

I see practitioners on social media forums providing brief synopses for complicated cases, asking for specific supplement and dosage advice on how to treat from their peers. I also frequently see patients who have seen other practitioners that tell me they saw no improvement in their presenting digestive symptoms, complaining that new symptoms appeared or that their health deteriorated. When it comes to the gut microbiome, there are a few common errors I see practitioners make when addressing imbalances with their patients. Thankfully, these errors can be addressed and, with practice, applied to benefit patient care.

Inadvertently promoting loss of microbiome diversity

Small intestinal bacterial overgrowth (SIBO) protocols often involve multiple rounds of antibiotics. A 2007 review in The ISME Journal looked at the long-term implications of antibiotic administration on the microbiota and concluded that long-term impacts can persist for up to two years post-treatment, including a significant negative impact to the Bacteroides community. A 2017 observational study in Clinical Nutrition ESPEN demonstrated that a classic ketogenic diet significantly increased Desulfovibrio species, specifically hydrogen sulfide gas formation in the gut.

I’ve also seen patients diagnosed with irritable bowel syndrome (IBS) who have been put on a long-term, restrictive low–fermentable oligo-, di-, and monosaccharide and polyol (FODMAP) diet for many years rather than a few months. By restricting the diet for long periods of time and removing prebiotic foods, we can see significant microbiota alteration, which can ultimately lead to loss of oral tolerance and increased reactivity to foods. Increased reactivity can make patients fearful of some foods, especially if a patient has experienced Herxheimer reactions in the past.

Rushing through complex concepts with patients

Patients are often eager to see results quickly. The practitioner should not be encouraging drastic change from the outset, but rather make cautious adjustments at the start, ensuring detoxification pathways and nutrient assimilation is supported. I often start with by making some dietary adjustments. Supplementally, I always start with digestive support, including enzymes and butyrate. I bring in omegas and binders and prioritize mineral and vitamin deficiencies. Supplements are introduced slowly and in small doses in sensitive patients. If a patient is in pain or not sleeping, this needs to be addressed and if possible, resolved quickly to facilitate healing.

When budget allows, I prefer that appropriate testing is performed to bring in more targeted treatment strategies. I also provide patients with additional resources around lifestyle changes and ensure that I have explained as clearly as possible what I think is happening, and what the next steps are for them so they understand the process, and what to expect.

When supplementing a patient with binders, or prebiotic fibers to mitigate die off and support preferential reinoculation of the microbiome, it’s essential to ensure the bowels are moving daily. Adequate magnesium supplementation to tolerance can help with this, along with castor oil packs or even basic castor oil massage if a patient doesn’t have the time or inclination to sit with a pack. In addition, ileocecal valve massage can be helpful to ensure bowel motility. A 2012 pilot study in the World Journal of Gastroenterology discussed defective ileocecal valve reflex found in patients with positive lactulose SIBO breath tests.

I also often use tea blends to provide detoxification drainage and antihistaminic support. Useful herbs to include are plantain (Plantago major), cleavers (Galium aparine), and nettle (Urtica dioica).

Using aggressive herbal protocols and dosages or unsuitable compounds

I’ve seen many patients who’ve been instructed to take essential oils internally by clinicians with no aromatherapy training or high doses of essential oil-based supplements for months at a time. I have also seen berberine negatively affect the microbiome by wiping out Bifidobacterium populations when taken long-term.

It’s also important to consider the phytoconstituents present in the herbs or supplements that a patient might be taking, rather than using a prescriptive agent that came up as sensitive on a stool test and how that might affect physiological function or if it might interact with nutrient absorption. For example, if a patient who is prone to constipation is taking high volumes of tannin-rich antimicrobial herbs such as bearberry (Arctostaphylos uva-ursi), or black walnut (Juglans nigra), their constipation might be significantly exacerbated, as tannins can dry out mucosal membranes by inhibiting cellular secretions and reducing peristaltic activity in the gut. Furthermore, tannins can interact with medications and inhibit absorption of nutrients. A 1998 paper in Food Chemistry also demonstrated that tannins can also interfere with iron absorption.

I avoid sulfur-containing herbs such as barberry (Berberis vulgaris) to preemptively avoid the possibility of patient reactivity, as these can aggravate the patient and create symptoms if a patient has high levels of sulfidogenic bacteria such as Desulfovibrio species in the gut, or developed sulfur sensitivity due to blocks in their detoxification pathways.

A nine-year-old boy I recently took on as a patient experienced significant die-off symptom, which his previous practitioner had tried to mitigate by giving him supplemental glutathione. In my clinical experience, glutathione, garlic, and betaine hydrochloride to clear dysbiosis, support detoxification, and mitigate hypochlorhydria are often be poorly tolerated so are best avoided until sulfur sensitivity can be determined or microbiome assessed. Patients often have high levels of sulfidogenic bacteria present in the gut, poor detoxification pathways. Common signs and symptoms of sulfur intolerance can often be mistaken for allergies or histamine intolerance, and include urticaria, nausea, brain fog, fatigue, and digestive disturbance.

Case Study

A middle-aged, female patient with type two diabetes mellitus historically controlled through diet, lifelong asthma, a personal history of gallstones, and a notable family history of colon cancer came to me after she had been to see a nutritionist. She had been diagnosed with infective colitis following a serious bout of food poisoning about six months prior, which had been treated with multiple courses of antibiotics by her primary care physician. She had since then lost a significant amount of weight and her bowels had become uncontrollable. She became anxious about leaving the house as she was experiencing bowel urgency, which has become more of an issue due to lack of availability of public restrooms and was affecting her ability to work as a nurse in a shift pattern.

Her previous nutritionist recommended that she follow a ketogenic diet to mitigate colon cancer risk and improve insulin sensitivity. They gave the patient probiotics and an ox bile supplement based on her history of gallstones. The patient was not provided with specific advice, and as a result, ate a diet high in dairy and meat products, as these are heavily featured in many ketogenic recipes online. She followed the diet for two months before switching over to work with me. In that period, her digestive health deteriorated, she experienced more gas, bloating, and irregular bowel movements with more diarrhea, her glucose control had worsened significantly during the day, her sleep shortened, and she became fatigued and irritable. Her stool test indicated high levels of Desulfovibrio species, Bilophila wardsworthia, Hafnia alvei, and Prevotella copri, the latter of which has also been associated with insulin resistance. Her results also indicated enterotoxigenic Bacteroides fragilis.

For this patient, a ketogenic diet high in saturated fats increased hydrogen sulfide gas and aggravated her digestive issues. A 2000 clinical trial in The American Journal of Clinical Nutrition also demonstrated that a high-meat diet can significantly increase hydrogen sulfide gas production, so even a traditional paleo diet wouldn’t be appropriate. A 2018 article in Nature Communications discussed how dietary lipids and subsequent bile production can promote the growth of Bilophila wadsworthia, a sulfidogenic, bile-resistant pathobiont commonly found in patients eating a diet high in animal fat and protein that promotes inflammation, as well as intestinal permeability, and has been shown to induce dysglycemia, and hepatic steatosis.

As deconjugated bile salts are reabsorbed in the small intestine, this can exacerbate fat malabsorption and create deficiencies in fat-soluble vitamins, such as vitamins A and D, key for immune regulation. I would never have advised this patient to transition to a ketogenic diet until their gut had stabilized and we had seen some test results. I would always eliminate dairy and red meat in a patient with a family history of colon cancer, but even our work temporarily restricting large quantities of high sulfur foods and any foods containing sulfur-based preservatives or sulfites helped to dramatically reduce inflammation.  I used enzymes and supported fat absorption with lipase rather than using cholagogue herbs or ox bile supplementation. One of her biggest personal stressors had been her physical appearance, as the patient had lost around 22 pounds in that six-month period, and she said she did not feel like herself.

I asked her to follow a low-sulfur, low-histamine diet for two weeks alongside foundational supplements such as a binder to mitigate die off and molybdenum to support digestion, detoxification, and sulfur metabolism. We then started to open up the diet to increased microbiome diversity, by introducing the foods that my patient missed most first and introducing one or two foods daily. At the one-month mark, the patient had not experienced any uncomfortable episodes, was sleeping better and felt more energized. We then brought in polyphenol-rich green tea extract (Camellia sinensis) in supplement capsule form, alongside a tea blend of blackcurrant leaf (Ribes nigrum), oregano (Origanum vulgare), pomegranate (Punica granatum), and marshmallow (Althaea officinalis) to further soothe, support and stabilize the microbiome.

At the two-month mark, we introduced a gentle antimicrobial tincture protocol, including herbs such as marigold (Calendula officinalis), cinnamon (Cinnamomum verum) and rosemary (Rosmarinus officinalis) to address the toxin-producing and dysbiotic bacteria present in her digestive tract. I explained that the patient should introduce the herbs slowly and gradually increase the dose, evaporating the alcohol off if necessary and increasing the frequency and dosage of the binder and fish oil if she experienced any adverse symptoms.

At the three-month mark, the patient happily reported that she regained most of the weight she had lost, and her family and partner were commenting on how she looked more like herself again. Her bloodwork indicated an improvement in glycemic control and lipids, and she no longer needed to use her inhaler daily. Sleep and energy levels are better, and her primary digestive complaints have been resolved.

References

Dukowicz, A.C., Lacy B.E., and Levine G.M. (2007) Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & Hepatology. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099351/#B44

Jernberg, C., Löfmark, S., Edlund, C., and Jansson J.K. (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME journal: Multidisciplinary Journal of Microbial Ecology. Retrieved from: https://doi.org/10.1038/ismej.2007.3

Magee, E.A., Richardson, C.J., Hughes, R., Cummings, J.H. (2000) Contribution of dietary protein to sulfide production in the large intestine: an in vitro and a controlled feeding study in humans. The American Journal of Clinical Nutrition. Retrieved from: https://doi.org/10.1093/ajcn/72.6.1488

Miller, L.S., Vegesna, A.K., Sampath, A.M., Prabhu, S., Kotapati, S.K.,  Makipour, K. (2012) Ileocecal valve dysfunction in small intestinal bacterial overgrowth: a pilot study. World Journal of Gastroenterology. Retrieved from: https://doi.org/10.3748/wjg.v18.i46.6801

Natividad, J.M., Lamas, B., Pham, H.P., Michel, M.L., Rainteau, D., Bridonneau, C., da Costa, G., van Hylckama, Vlieg J., Sovran, B., Chamignon, C., Planchais, J., Richard, M.L., Langella, P., Veiga, P., and Sokol, H. (2018) Bilophila wadsworthia aggravates high fat diet induced metabolic dysfunctions in mice. Nature Communications. Retrieved from: https://doi.org/10.1038/s41467-018-05249-7

South, P.K. and Miller, D.D. (1998) Iron binding by tannic acid: effects of selected ligands, Food Chemistry. Retrieved from: https://doi.org/10.1016/S0308-8146(98)00040-5.

Tagliabue, A., Ferraris, C., Uggeri, F., Trentani, C., Bertoli, S., de Giorgis, V., Veggiotti, P.,  and Elli, M. (2017) Short-term impact of a classical ketogenic diet on gut microbiota in GLUT1 Deficiency Syndrome: A 3-month prospective observational study. Clinical Nutrition ESPEN. Retrieved from: https://doi.org/10.1016/j.clnesp.2016.11.003

Virally-Monod, M., Tielmans D., Kevorkian J.P., Bouhnik Y., Flourie B., Porokhov B., Ajzenberg C., Warnet A., and Guillausseau P.J. (1998) Chronic diarrhoea and diabetes mellitus: prevalence of small intestinal bacterial overgrowth. Diabetes & Metabolism. Retrieved from: https://pubmed.ncbi.nlm.nih.gov/9932220/