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SIBO | Small Intestinal Bacterial Overgrowth

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What is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth. It is a condition characterized by an abnormal increase in the number and/or type of bacteria in the small intestine. Normally, the small intestine has relatively low levels of bacteria compared to the colon. However, in SIBO, bacteria (or archea) that are normally found in the colon migrate into the small intestine and proliferate, leading to an overgrowth.

What are the symptoms of SIBO?

This overgrowth of bacteria in the small intestine can interfere with the normal digestive processes and nutrient absorption, causing a range of symptoms. Common symptoms of SIBO include bloating and abdominal pain after eating, diarrhea, constipation, and malabsorption of nutrients, which can lead to nutritional deficiencies.

The normal transit of food in the intestines vs in SIBO

An overgrowth of bacteria that produce hydrogen often cause diarrhea and a faster transit time, as the small intestine is very sensitive to hydrogen. Alternatively, people with an archea overgrowth (which is not technically a bacteria), produce more methane. Archea can feed off hydrogen to produce methane, so it is common for people to have a combination of both. But when methane levels increase in the small intestine, it leads to slow transit time and constipation.


What are the differences between SIBO and IBS? 

SIBO is one of the main causes of IBS, with about 75% of IBS sufferers experiencing SIBO. As IBS is a syndrome, there are multiple underlying causes, stress and anxiety being a very common cause.

Need help figuring out if you have SIBO?

How to figure out if you have SIBO

How is SIBO diagnosed? 

The gold standard for diagnosing SIBO is a breath test that measures the presence of certain gasses produced by bacteria or archea in the small intestine. If there are high levels of hydrogen in the breath, there is likely an overgrowth of bacteria, whereas if there are high levels of methane, there is likely an overgrowth of archea. 


How do you test for SIBO? 

There are two different options for SIBO testing- glucose or lactulose breath tests, each with their own pros and cons. Patients will drink one of these solutions as a method to feed the overgrowth in the small intestine. Then over the course of 2-3 hours, a breath test will be performed every 15-20 minutes to measure the levels of hydrogen and methane in the breath, based on fermentation of the substrate. 


Pros and cons of Glucose and Lactulose testing: 

Glucose- is absorbable in the small intestine so it’s unlikely to pick up colonic fermentation. But since it may not make it to the end of the small intestine, there is a risk of false negatives if the overgrowth is only located distally.

Lactulose- is a non-absorbable sugar, so it will make it all the way through the GI tract, therefore feeding any bacteria or archea along the way. The downside to lactulose is that it is a laxative, so it may give false positives as it may cause a faster transit time, allowing for the colonic bacteria to ferment the lactulose. 

There is the option of testing with a one time use breath test which can be completed in the comfort of your own home. Alternatively, we prefer using a Food Marble as this is a repeatable at-home breath test, so it can be useful at retesting after treatment to assess progress. 

What Causes SIBO?

  • Infection/ food poisoning 
      • This is the most common cause, and one of the more difficult root causes to address. The reason for this is that the main infections that cause food poisoning release toxins that the body creates antibodies for. In addition to attacking the toxins, these antibodies will often attack nerve cells in the small intestine known as the migrating motor complex (MMC). This can lead to constipation as the nerve damage starts to slow down motility, leading to bacteria migrating up into the small intestine. 
  • Other causes that can slow down motility are:
    • Autoimmunity, traumatic brain injury, hypothyroidism, diabetes, chronic antibiotic use, hypermobility disorder such as ehlers danlos syndrome. The bottom line is- anything that slows down motility can lead to overgrowth in the small intestine. 
  • Lack of digestive enzymes- leading to less breakdown and absorption of our food, allowing it to sit in the small intestine to feed an overgrowth of bacteria. This especially happens with certain types of carbohydrates like lactose, inulin, sorbitol and fructose.
  • Lack of other digestive secretions such as bile or stomach acid– this is commonly seen when we eat in a stressed state as we do not activate the “rest and digest” mode
  • Stress: when we are stressed frequently, our nervous system runs in a mode called the sympathetic nervous system. The downside to this is that we will not activate the vagus nerve in this mode, which is a very important nerve for activating digestive secretions, leading to all of the above problems
  • Impaired outflow: abdominal surgery or trauma, diverticulosis, endometriosis or any other adhesions in the intestines can cause changes in how we excrete stool, and can lead to residual stool stuck in the intestines. This can become a hub for bacteria to thrive and overgrow leading to SIBO.

Medications: PPIs, antibiotics, antidepressants, antispasmodics, opiates, narcotics, antidiarrheal medication can also lead to SIBO if used for long periods of time.

What are the treatment options for SIBO?

Treatment often involves antibiotics or herbal antimicrobials to reduce the bacterial overgrowth, as well as dietary changes to manage symptoms and prevent recurrence.


Pharmaceutical route

There are a variety of antibiotics that have been studied in SIBO, but Rifaximin is the most well researched and safe option. This medication is not absorbed in the intestine, so it works well to locally kill both archea and bacteria. 


Herbal antimicrobials

The other option instead of pharmaceutical antibiotics is to use herbal medicine, which has been studied to be as effective as Rifaximin in clinical trials. There are a variety of different herbs used to treat an overgrowth, some with higher affinities to kill off bacteria vs archea. In general the most common herbs to use for each SIBO subtype include:

Hydrogen predominant: berberine, neem

Methane predominant: oregano, allicin, cinnamon, thyme

Depending on the level of overgrowth, the need for multiple rounds of antimicrobials varies. It is important to not just keep repeating the same antimicrobial with each course, as bacteria and archea are smart and can become resistant to treatment, just the same as with pharmaceutical antibiotics. 


Nutritional Treatments

In addition to killing off an overgrowth, it is very helpful to also starve them off by limiting their favorite foods- FODMAPs. FODMAPs are a group of fermentable sugars that bacteria and archea love to consume and turn into gas- leading to the bloating and uncomfortable symptoms seen in SIBO. There are a wide variety of foods that fall under the high FODMAP category, with onions, garlic, potatoes and mushrooms, as well as starchy bread and pasta being the highest. 

Although many patients feel significant relief of symptoms with a low FODMAP diet, It is important to not rely on this type of diet permanently. This is because removing those fermentable sugars chronically can lead to starving off the good bacteria that we want in the LARGE intestine. The bacteria in the large intestine help create anti-inflammatory molecules like short chain fatty acids which are important for whole body health. In addition to this, the low FODMAP diet is quite restrictive, and can lead to reduced quality of life and nutrient deficiencies if relying on it for too long. It is therefore very useful to restrict when treating SIBO, but it’s important to reintroduce FODMAPS back into the diet slowly once the SIBO is resolved. 


Other natural treatments for SIBO

Motility agents

Motility agents, also known as prokinetics, can be helpful at stimulating the MMC, and help the nerve cells of the intestine increase stool movement. The most common natural motility agents include ginger, vitamin B6, 5-HTP, and artichoke.


Osmotic laxatives

In addition to motility agents, it can be helpful to add in a mild osmotic laxative in patients with chronic constipation. Magnesium citrate is an osmotic laxative, therefore it helps draw water into the intestine and help move stool. It is important to stay hydrated when taking this form of magnesium as drawing too much water into the intestines can lead to dehydration.


Can probiotics help with SIBO? 

It is important to introduce probiotics at the right time with SIBO. Often probiotics can initially make things worse, or do nothing at all when starting on a SIBO treatment. If we take them during the anti-microbial phase, they will often also be killed off making it an expensive supplement with little benefit. A SIBO protocol usually involves a re-introduction phase after the SIBO has been killed off, where the “good” bacteria are re-introduced. This is where probiotics come in handy as they will help bring in the good, and help re-shape a healthy microbiome for the long term. 

What are the long-term effects of SIBO if left untreated?

If left untreated, SIBO can wreck a lot of havoc on your body. Not only are nutritional deficiencies highly likely, but chronic inflammation of the intestine can lead to damage of intestinal cells. 

It’s important to note that SIBO can be a chronic condition, and its management may require ongoing attention to prevent relapses and address underlying issues. 

If you suspect you have SIBO or are experiencing digestive symptoms, it’s recommended to consult with a healthcare professional for proper diagnosis and guidance on treatment options. 

Dr. Miller has a special focus in gut health in her practice, and sees a large population of SIBO and chronic bloating patients. For more information on how Dr. Miller could help you with your chronic bloating or suspected SIBO, feel free to book in a free roadmap call  with her.

Dr. Elizabeth Miller Naturopathic Doctor

Your Doctor: Meet Dr. Miller

Dr. Miller has a special focus in gut health in her practice, and sees a large population of SIBO and chronic bloating patients. 

Dr. Miller is a Naturopathic Doctor who has a special focus on digestion and hormone health. She completed her doctor or naturopathic medicine degree at the Canadian College of Naturopathic Medicine, and holds a Master’s and Bachelor’s of science in Human Health and Nutrition from the University of Guelph. Her extensive knowledge of nutrition and her strong foundation in scientific research allows for a very thorough approach to your care.

Dr. Miller discovered naturopathic medicine after struggling with chronic irritable bowel syndrome for many years. She saw multiple doctors with no solution, as IBS was not well understood at the time. To take matters into her own hands, she devoted her master’s thesis to IBS research, and from here was introduced to naturopathic medicine which helped her immensely. Today Dr. Miller devotes a large part of her practice to treating digestive concerns and chronic bloating as it is very near and dear to her heart. Her goal is to blend the balance of nutrition, modern research, lab testing and traditional medicine to get to the root of her patient’s IBS and chronic bloating.

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