Small Intestinal Bacterial Overgrowth (SIBO) and the Gut Microbiome

by Melissa Castaneda   

Welcome to a story of gut health and a journey to restoration. I had a dull pain on my left side for 18 months. While waiting for an appointment date to see a gastroenterologist, I requested some vitamin panel tests from my primary care physician, and found my B12 levels were high, indicating a malabsorption issue. This type of disorder is often found in conjunction with a form of gut dysbiosis called small intestinal bacterial overgrowth (SIBO). The first thing the gastroenterologist asked was, “Have you heard of SIBO?”

He later elaborated that should he write “SIBO” into my chart, I would be “pegged in the system forever for rounds of antibiotics, and that’s the worst thing we could do.” The fact that he was hesitant to give me an official diagnosis led me to research more on my own.  

I learned that the studies on SIBO and other forms of microbial dysbiosis have large collective data gaps, which creates a problem in formulating a cohesive therapeutic approach. However, the research shows that nutritional therapy, with or without the use of herbal or conventional antibiotics (depending on the severity of your case), is an effective way to alter the condition of your gut. Every bite we take has an epigenetic effect. The beauty of epigenetics is our ability to influence the way our genes are activated or suppressed. One way to do this in a positive manner is by being a diet snob and rejecting poor-quality commercial food.


SIBO is a disruption of the intestinal microbiota, resulting in a state of dysbiosis. Most often, it occurs when bacteria that should normally only take up residence in your large intestine migrate into the small intestine. Left unchecked, this displaced colony of bacteria can cause malabsorption of nutrients, among a myriad of other issues. When your beneficial colonies of bacteria are depleted or completely annihilated by the overgrowth of pathogenic bacteria, they can no longer fulfill their functions or their performance is severely altered. The National Institutes of Health says this about gut dysbiosis: “The intestinal microbiota is involved in the production of vitamins, the activation or inactivation of bioactive food components such as isoflavanoids and plant lignans, the conversion of prodrugs to their bioactive forms, and the transformation of bile acids and xenobiotics.”1

Beneficial colonies of bacteria perform vital functions that support everything from cellular repair to cognitive and immune functions through the chemical reactions they initiate by converting food into usable molecules. SIBO may be one of the underlying causes of inflammatory bowel disease, autoimmune disorders, and other illnesses. 


Nutritional therapy for SIBO consists of a diet meant to starve the pathogenic bacteria in your small intestine. To do this, low-FODMAP, gluten-free, sugar-free, and dairy-free diets can be adopted. These diets restrict, to varying degrees, the intake of fermentable and other reactive foods. 

The low-FODMAP diet aims to deprive the pathogenic bacteria of fermentables that allow them to thrive, so that their colonies begin to die off and the suppressed healthy colonies (if they are still present at all) begin to repopulate the small intestine. If you have caught your SIBO early enough, this may be all that you need for the gut to begin to heal. If you have not and are already experiencing the effects of nutrient malabsorption, you may also need other gut-healing protocols to address what is usually referred to as leaky gut

A gluten-free diet helps prevent inflammatory responses in the gastrointestinal tract, which is already stressed and quite possibly exhibiting signs of non-celiac gluten sensitivity. This condition occurs because of the difficulties gluten presents in the digestive tract. Gluten does not break down into the traditional amino acids that occur during digestion; rather it breaks down into a difficult-to-digest oligopeptide chain that can trigger immune and inflammatory responses.2  Sugar- and dairy-free diets further remove known inflammatory foods. The incredible power of the gut to heal itself is unparalleled, and diet is the simplest consideration on the path to restoring balance to the gut microbiome.


According to a 1990 publication, breath tests were an inadequate alternative to the then-gold standard of SIBO diagnosis, which was culture analysis of jejunal aspirates by means of endoscopy. While considered minimally invasive, an endoscopy is not necessarily a “painless” procedure, and current views have shifted. As of 2017, a study on hydrogen- and methane-based breath testing suggested that “breath tests (BTs) are important for the diagnosis of carbohydrate maldigestion syndromes and small intestinal bacterial overgrowth.”3   

It’s likely this method became the preferred diagnostic medium due to its non-invasive nature and accessibility. The frequently used lactulose breath test measures the levels of hydrogen and methane that your body emits at metered intervals after consuming a solution. This can help determine which fermentables you need to completely remove from your diet or closely monitor. It is the most common testing method used by general practitioners and osteopaths. If you choose to consult a functional medicine physician or naturopath, you may have the option of various microbiome screenings. These screenings are usually done by labs that analyze specific bacterial strains known to reside in the large and small intestines. They then compare your active levels of these strains against known “normal” levels to determine your level of dysbiosis. This is extremely useful in helping determine how advanced a microbial imbalance might be and ultimately helps a provider tailor treatment options to a specific individual.


The majority of Western-centered medical practices take the conventional antibiotic approach, which consists of an initial round of antibiotics, followed by additional rounds should the desired results not manifest. This therapy may provide varying degrees of relief, but it effectively destroys the healthy populations of gut bacteria that are necessary for balanced digestive function. When the colonies of beneficial bacteria are decimated, your body has to create entirely new healthy colonies, which can take much longer than simply rebuilding from existing colonies. 

If antibiotics are your treatment approach, keep in mind the importance of taking probiotics when undergoing antibiotic therapies. In 2014, a pilot study of probiotics taken in conjunction with antibiotics in patients with SIBO concluded, “Based on the preliminary data it seems that adding lactol probiotic to the maintenance therapy of small intestinal bacterial overgrowth patients on routine antibiotic therapy will be beneficial in preventing the complications of this syndrome.”4 

If you wish to pursue a natural approach instead of conventional antibiotic therapy, it is important to have a knowlegeable physician, naturopath, dietitian, or other professional counsel you as to proper dosing before you take any form of herbal therapy intended to be used in place of antibiotics. Herbal remedies can be extremely effective, but these remedies are potent forms of medicine in the most functional of senses and should be respected as such.  

Many alternative treatment options focus on eliminating the bacterial overgrowth in your small intestine by means of combinations of concentrated essential oils and alkalizing compounds such as berberines to help destroy the pathogenic microbial colonies, essentially restoring balance to your intestinal microbiome. These compounds can also be used in conjunction with digestive enzymes to help support absorption of vitamins and other essential nutrients during treatment.


It’s important to note that, with SIBO, the use of a probiotic may or may not be beneficial depending on your state of dysbiosis.  It is also thought that prolonged low-FODMAP diets can rob your system of essential food-based prebiotics, making your situation worse. If your healthcare provider determines you will benefit from probiotics, a formula that includes Saccharomyces boulardii might be prescribed. While there are many strains of probiotic yeast, the Saccharomyces boulardii strain (originally extracted from the lychee fruit and also found in mangosteen fruits) works synergistically with other probiotics, and reduces the ability of pathogenic bacteria to adhere to intestinal cells. It also stimulates your intestinal tract to produce enzymes necessary for nutrient absorption, supports recolonization of healthy gut bacteria, and helps prevent adverse reactions that you may experience with conventional and natural antibiotic therapies.


Care should be taken with this particular strain if you have a known allergy to brewer’s yeast. Many probiotic blends will also include strains such as Lactobacillus acidophilus, Lactobacillus plantarum, and/or Bifidobacterium lactis. The precise blends are manufacturer specific, but these strains are present throughout your intestinal tract and body, and thus are usually included to help support and recolonize depleted populations. There are over 400 strains of bacteria found throughout the body, so if you do not see these exact strains in your supplement, consult your healthcare provider. Maybe you were prescribed a different blend for specific reasons, or maybe the discussion will determine that these additional strains can be added into your recovery plan. Dosing can be advised by your provider.


The factors that can negatively affect the balance of your gut microbiota include: antibiotic usage (including any antibiotic therapy used to treat a previous ailment), antidiarrheal medications, fiber oversupplementation, poor functional diet, and the use of proton pump inhibitors. These are all factors that we control. It has become common to recommend or even self-prescribe an antidiarrheal or fiber supplement without fully understanding and investigating the underlying causation of digestive woes. While there may be a sense of instant gratification with these remedies, it’s safe to say that if any original symptoms continue to manifest after treatment, continuing to ignore them can lead to any number of aggravated issues, depending on the underlying problem.

Diet plays a major role in maintaining the balance of your gut microbiome. Living a life of excess or consuming an imbalanced diet for extended periods of time can starve your body of the vitamins and other essential nutrients it needs to function. This can create states of imbalance in your gut, which can allow overgrowth to occur.  


  • IBD/IBS-like symptoms
  • Allergies or food sensitivities
  • Acne
  • Thinning hair
  • Hormonal changes/mood swings
  • Difficulty gaining or losing weight
  • Difficulty sleeping
  • Emotional distress 
  • Depression
  • Anxiety
  • Numbness and tingling in the extremities
  • Joint pain
  • Headaches
  • Brain fog
  • Nausea


I have experienced all of these symptoms, accompanied by excessive fatigue. I have been on a low-FODMAP diet since my initial gastroenterologist visit in July 2017, and I am on week nine of twelve of a physician-guided herbal antibiotic regimen and a dairy-, gluten-, and mainly sugar-free diet. I say mainly because sugars are in almost everything, and, while I maintain a fairly strict diet, I am human and indulge in something sweet now and again. The constant ache on my left side went away within the first month on the low-FODMAP diet, but I was still having trouble losing excess weight and felt that my persistent headaches were being triggered by something I was consuming. On week three of my dairy- and sugar-free diet, I cheated with some chocolate candies, and I woke up with a throbbing headache the next morning. This illustrates the importance of these types of elimination diets.

Carefully following elimination diets and documenting your symptoms are important in helping you discover your triggers, although the SIBO elimination diets are so different from a “normal” Western diet that they create a challenge for many people. All of a sudden, a person has to scrutinize labels and find alternatives to many basic foods they might have found comfort in. The healthy outcome is worth it, however. It’s also worth it to invest in seeing a functional medicine physician or nutritionist to help guide you. For me, just being on the low-FODMAP diet—and now boosting my efforts by eliminating sugar, gluten, and dairy—has relieved the persistent throbbing headaches, most of the fatigue and brain fog, and the constant abdominal discomfort. This journey has led to a long-awaited and warmly welcomed relief. ∆  

This article was printed in the May/June 2018 issue of Well Being Journal, Vol. 27, No. 3. See more at, including a special collection on digestive health in “Special Collections.”

Melissa Castaneda is a wellness advocate. She grew up in a family that used herbal remedies, and after being diagnosed with a connective tissue disorder called Ehlers Danlos Syndrome, she began to research and write about nutrition and supplements. For more, visit her on Instagram at @plantedinnature and @eds_needs, and on the web at and Contact:



1. Carding S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health and Disease, 26(1),

2. New, J. (2013). How is gluten digested?

3. Rezaie, A., Buresi, M., Lembo, A., Lin, H., McCallum, R., Rao, S., et al. (2017). Hydrogen and methane-based breath testing in gastrointestinal disorders: the North American consensus. The American Journal of Gastroenterology, 112(5), 775–784.

4. Khalighi, A. R., Khalighi, M. R., Behdani, R., Jamali, J., Khosravi, A., Kouhestani, S., et al. (2014). Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO) - a pilot study. The Indian Journal of Medical Research, 140(5), 604–608.