What is Small Intestinal Bowel overgrowth (SIBO)

Many people who experience gas or bloating regularly or are dealing with IBS, may have Small Intestinal Bacterial Overgrowth (SIBO). Small Intestinal Bacterial Overgrowth, or SIBO, occurs when the bacteria in your small intestine become unbalanced and overgrow.

The bacteria in your GI tract make up your gut microbiome and play a vital role in your immune system, thyroid function, mood, bone health, nervous system health and overall wellbeing. Scientists have now discovered that the gut microbiome contains tens of trillions of microorganisms, including up to 1,000 different species of bacteria with over 3 million genes. Most of our gut bacteria is meant to be located in our large intestine and colon, where they help break down food, synthesise vitamins, and eliminate waste. When bacteria normally found in the large intestine and colon begin to migrate upwards and colonise the small intestine, SIBO occurs. Small intestinal bacterial overgrowth can also occur when there is an overgrowth of otherwise normal bacteria in the small intestine itself.

As the bacteria feed off of undigested food in your small intestine, the carbohydrates ferment and produce hydrogen. Hydrogen can feed single-celled organisms in your small bowel called archaea, which then produce methane. An excess amount of hydrogen, methane, or both  as well as hydrogen sulphide can occur in your digestive system.

The excess gas in your GI tract can then lead to gas and bloating which can be severe. Other symptoms include:

  • Diarrhoea (methane dominant)
  • Constipation (more common with Hydrogen dominant SIBO)
  • Fast transit time (hydrogen dominant)
  • Rotten egg smell (Hydrogen sulphide dominant SIBO)
  • Abdominal pain or cramping
  • Irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD). Many IBS patients have SIBO
  • Food intolerances such as gluten, casein, lactose, fructose
  • Histamine intolerance. SIBO is often the root cause of histamine intolerance which can lead to a plethora of symptoms, including many listed below
  • Chronic illnesses such as fibromyalgia, chronic fatigue syndrome, diabetes, neuromuscular disorders, and autoimmune diseases
  • Vitamin and mineral deficiencies
  • Fat malabsorption (pale, bulky, and smelly stools are signs of fat malabsorption)
  • Acne rosacea and other skin issues
  • Leaky gut
  • Restless legs syndrome
  • Insomnia
  • Headaches
  • Fatigue
  • Itching
  • Anxiety
  • Hypertension
  • Hives
  • Elevated inflammation

Sometimes people show no physical signs at all, some people have one symptom others have many or them all. Approximately 6-15% of healthy, people with no symptoms, and roughly 80% of people with IBS, actually suffer from SIBO.

What causes bacteria overgrowth?

After enzymes break down our food, our gut moves the food through our digestive tract from the stomach to the small intestine and to the colon. In a healthy gut, bacteria gets passed through the digestive tract along with food to its final destination in the colon.  The following risk factors interfere with this process:

  • A food poisoning episode - acute gastroenteritis
  • A diet high in sugar, refined carbohydrates as well as legumes and so called healthy grains such as brown rice, quinoa, alcohol, and other high-carbohydrate foods you eat or drink.
  • Stress and nervous system dysfunction, especially chronic stress. When the body is in the sympathetic fight-or-flight state, gastric function is altered. We are not in the rest-and-digest state anymore. This also affects the enteric nervous system that controls the migrating motor complex.
  • Damaged nerves or muscles in the gut resulting in leftover bacteria in the small intestine. Some autoimmune diseases such as scleroderma can affect the muscles in the gut as can diabetes, allowing SIBO to develop.
  • Diabetes. The oxidative damage caused by high blood sugar in diabetes can lead to deterioration of vision, kidney function and peripheral blood vessels and also damage the nerves that regulate and control intestinal migrating motor complexes.
  • Low thyroid function can affect all cells of the body, including the cells of the GI tract. Hypothyroid can reduce the activity within the gastrointestinal tract, slowing the migrating motor complexes that trigger peristalsis.
  • Physical obstructions in the gut, and abdominal adhesions such as scarring from surgeries or Crohn’s disease can create an obstruction or distortion of the intestines and/or impair the enteric nervous system’s migrating motor complex, both of which can predispose to SIBO.
  • Diverticulitis causes tiny pouches that can form in the wall of the small intestine which can collect bacteria.
  • Medications including antibiotics, acid-blocking drugs such as Omeprazole, NSAIDS such as Aspirin, Ibuprofen and steroids which can disrupt the normal gut flora. Research has shown even one dose can disrupt the microbiome.
  • Slowed gut motility.
  • Depressed immunity. Various immunodeficiency syndromes have been associated with increased risk for bacterial overgrowth, including IgA deficiency. Secretory IgA in the gastrointestinal tract is the largest fraction of immunoglobulins secreted in the body, and aids in preventing bacterial proliferation.
  • Stealth infections. The potential complications arising from acute or chronic infections from lyme or other tick co-infections are many, and include gut dysfunction. Infections such as varicella zoster, Epstein-Bar virus, and Lyme disease can all disrupt gut motility.
  • Excess estrogen. Excess estrogens can inhibit the excretion of bile salts from the liver into the intestines. Bile salts have an antimicrobial activity and their deficiency can be a predisposing factor for SIBO. Estrogen also delays gastric emptying and motility.
  • A disruption of the migrating motor complex encourages bacterial overgrowth and prevents excess bacteria from being cleared out of the small intestine

What is the Migrating Motor Complex?

The migrating motor complex (MMC) is a distinct pattern of electromechanical activity observed in gastrointestinal smooth muscle during the periods between meals. It is thought to serve a "housekeeping" role and sweep residual undigested material through the digestive tube.

An increase in gastric, biliary and pancreatic secretion is also seen in conjunction with the motor activity. These secretions probably aid in the cleansing activity of the migrating motor complex and assist in preventing a buildup of bacterial populations in the proximal segments of the digestive tube.

The periodic nature of the MMC is thought to be controlled from the central nervous system and may be implemented in part by the enteric hormone motilin. Like real housekeeping, the MMC is readily overridden by "more important" processes - for example, eating will abolish a MMC and restore a digestive pattern of motility. So grazing inhibits MMC activity, as does chronic stress.

MMC activity can be noisy and can cause the “growling” noises one hears with an empty stomach.

Hydrogen vs Methane SIBO

The best way to describe hydrogen dominant SIBO is to think of it as the first “step” for where things can go wrong. 

When we’re healthy, food is broken down and absorbed through the small intestinal wall. SIBO is when there is too much bacteria there and/or the wrong bacteria in your small intestine. When that happens, food will ferment before it can be broken down. That process creates hydrogen gas as a byproduct, and thus leading to high levels of hydrogen and a positive SIBO breath test indicating hydrogen dominance.

SIBO can also cause an increase in methane levels. Your small intestines can also contain overgrowth of ancient single-cell organisms without a nucleus called archaea. Archaea are not bacteria and they deed off of hydrogen. They produce methane as a byproduct. This helps reduce the levels of hydrogen in the body. This is why you can have a negative hydrogen test or a flat line and still have SIBO. Archaea also slow motility which further exacerbates the problem.

Organisms like archaea which create methane are called methanogens. The process of forming methane is methanogenesis. Animals like cows rely on methanogen-forming archaea. Cows produce a huge amount of methane because of all the bacteria in their stomach which ferment grass. The archaea have an abundance of hydrogen from all the fermentation, they then proliferate and produce methane, which produces flatulence

process of methane production Process of methane production

Key Points about the Two main types of SIBO

  • SIBO can be methane-producing, hydrogen-producing, or both
  • Bacteria produces hydrogen. So SIBO produces hydrogen
  • Hydrogen feeds Archaea
  • Archaea produces methane
  • Carbohydrates feed SIBO, especially high FODMAPS carbs
  • Hydrogen SIBO usually causes diarrhoea
  • Methane SIBO usually causes constipation
  • Breath tests for SIBO will measure levels of methane and hydrogen
  • If your hydrogen levels are high, then you may have Hydrogen-dominant SIBO.
  • If your methane levels are high, then you may have Methane-dominant SIBO.
  • A diagnosis of Hydrogen SIBO or Methane SIBO doesn’t mean you only have that type of gas present.
  • You can have both types of gases, just one is more dominant than the other.

Hydrogen Sulphide Dominant SIBO

  • This is the third and most recently discovered type of SIBO and the research about how to test for this and treat it is still developing.
  • The human body uses sulphur for our cells and microbiome, and detoxes and excretes most of the byproducts of sulphur metabolism that it doesn’t need.
  • In a healthy person, small amounts of sulphur is converted into hydrogen sulphide.
  • If too much hydrogen sulphide is produced by our microbiome and our bodies natural ways of detoxifying it in the gut are overwhelmed, it can cause many health issues, including SIBO.
  • One telling symptom of hydrogen sulphide SIBO is gas that smells like rotten eggs.

Lab Testing and what results mean:

A breath Test is the gold standard for SIBO testing. It is the most accurate and it determines if the SIBO is hydrogen or methane dominant. After fasting for 12 hours, you breathe into a small balloon to measure baseline levels of hydrogen and methane. Then, you ingest a precise amount of sugar to feed the bacteria and repeat breath samples every 15 minutes for 3 or more hours to see if levels of hydrogen or methane increase. A comprehensive stool can also give us clues if we see elevated levels of all good bacteria. I routinely use stool testing to test for many different gut overgrowths such as Candida or other yeast overgrowth, small intestinal bacterial overgrowth, parasites, dysbiosis, inflammation, secretory IgA. However I still like to confirm SIBO with a great test is the results are not conclusive.

SIBO protocol

Step 1. Starve the Overgrown of Bacteria: The first step is to remove the foods that feed the bacteria in your small intestine including sugar, alcohol, and carbohydrates, this includes bread, biscuits, cake, crackers, pies, pasta as well as complex carbohydrates such as grains and legumes. Ultimately, your gut breaks these foods down into sugar, which feed the bacteria. A SIBO diet includes plenty of non-starchy vegetables as many as you can tolerate, leafy greens, lean proteins, and healthy fats, with minimal fruit. Limit healthy carbs from vegetables to 2 cups a day.

Step 2.Eradicate the bacteria: One can use an individualised precision prescription of herbal medicines and essential oils o ready prepared products containing extracts from tribulus, sweet wormwood, goldenseal, barberry, bearberry, neem, black walnut and essential oils. These options are a more natural and gentle way to eradicate the bacteria than antibiotics. Alternatively you can use an antibiotic called Rifaxamin that is very different to other antibiotics in that its actions stay in the gut. Rifaxamin is more effective with hydrogen-dominant SIBO, the dose is 550 mg three times daily for 2 weeks.  In my experience people tend to relapse more on traditional antibiotics than the herbal antibacterials.

Most of the archaea which produce methane are somewhat resistant to the antibiotics used to treat SIBO. So, if your problems are caused by archaea overgrowth, then taking those antibiotics aren’t likely going to cure your SIBO, even if you take multiple rounds.  Because of this, methane SIBO is definitely the most difficult to treat because of archaea’s resistance to antibiotics.

Step 3. Detoxify: Use a form of activated Charcoal, which helps encourages healthy detoxification pathways, helps encourage the binding and adsorption of toxins, promotes digestive comfort and relieves occasional gas.

Step 4. Take digestive enzymes to support digestion: I generally recommend Digestzyme from Invivo Healthcare. Digestive enzymes can help digest the poorly-digested, fermentable carbohydrates that produce the uncomfortable symptoms of SIBO.

Step 5 Replenish the gut microbiome: After eradicating the overgrowth we need to replenish the good bacteria in your gut which are so important for immunity, digestion, brain health and nutrient absorption. However, with SIBO you want to be super careful as many probiotics can exacerbate the SIBO. Often when you have an overgrowth of bacteria in your small intestine, it is the lactobacillus or bifidobacterium species. The majority of probiotic supplements contain these species, so using them adds to the all ready overgrown bacteria in your small intestine. Taking them often worsens symptoms if you have SIBO - which is  a clue that you have an overgrowth in your small intestines.

I recommend soil-based spore forming Probiotics such as Core biotic, Primalspore and Megaspore. Soil-based probiotics don’t colonise the small intestine or feed the bacteria already growing there as they don’t  contain lactobacillus or bifidobacterium strains, yet provide all the benefits of a probiotic.

We call all live a healthier more active, happy life free from chronic conditions, we just need the to learn how!

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