SIBO 101: A Comprehensive Guide to Small Intestinal Bacterial Overgrowth

Man holding stomach with SIBO abdominal pain

When an overgrowth of bacteria occurs in the small intestine, it is called SIBO (small intestinal bacterial overgrowth), and it may have negative effects on both the structure and function of the small intestine that can result in a wide array of disruptive physiological and psychological symptoms. The small bowel typically does not contain very much bacteria, so it should not be present there in large numbers. It houses less than 10,000 organisms per milliliter of fluid, compared to 1000,000,000 per milliliter fluid in the large colon, and the bacteria in the small bowel are different from those that inhabit the large intestine. Most bacteria in the small intestine is L. acidophilus. We have bacteria throughout the entire digestive tract from mouth to anus, but most of it resides in the colon.

This post is going to be the first in a series of three on this topic as this is a very complex condition that will take some time to cover. This week we will look at how SIBO develops, common symptoms, impact on health, and diagnosis. In the following weeks, we will look at diet, treatment, maintenance, and confounding factors like Candida overgrowth and H. pylori.

SIBO may occur as an overgrowth of the bacteria that normally inhabit the small intestine (L. acidophilus), but most often it is caused when bacteria that reside in the large intestine migrate into the small intestine. Put more simply, there is an increase in the number of bacteria and/or a change in the type of bacteria that are typically present. Overgrowth usually involves a variety of different types of bacteria, not just one. In contrast to many other bacterial infections, SIBO is not contagious. According to Dr. Allison Siebecker, one of the leading experts on SIBO, the species most commonly found in overgrowth include commensal anaerobes (Bacteroides 39%, Lactobacillus 25%, Clostridium 20%) and commensal aerobes (Streptococcus 60%, Escherichia coli 36%, Staphylococcus 13%, Klebsiella 11%, Escherichia coli 37%, Enterococcus spp 32%, Klebsiella pneumonia 24%, Proteus mirabilis 6.5%).

Organic Acids Test

The healthy bacteria that reside in the small bowel play a critical role in your health, because they protect us from pathogens, they help us digest food and absorb nutrients, produce digestive enzymes and nutrients like short-chain fatty acids, vitamin A, B12, K, and biotin, metabolize lipids, break down cholesterol, improve peristalsis and bowel transit time, and eliminate toxins and waste.

However, we don’t want a lot of bacteria in the small intestine, because that is where we digest our food and absorb our nutrients. If a lot of bacteria is present in this area, it will interfere with the digestion and absorption process. Being present in this area gives them premature access to our nutrients. Typically we get first dibs to our nutrients and they get what’s left over once it travels to the colon. If they are present in the small intestine, then they take the nutrients they want first and we can what’s left over. When they consume these nutrients before our own cells have a chance to obtain them, it can lead to a wide variety of nutritional deficiencies and negative consequences.

Bacteria need B12 and iron for their survival so these are the two most common deficiencies found in people with SIBO, but they also take calcium, magnesium, amino acids, and others. If a lot of diarrhea is occurring due to the bacteria, this can also contribute to malabsorption and malnutrition. Overgrowth of bacteria in the small bowel is the leading cause of fat malabsorption because it deconjugates bile salts that are needed for this process, which can also lead to deficiencies in fat-soluble vitamins like vitamin A and D. Bacteria also consume our disaccharide enzymes, which are needed to break down carbohydrates, leading to more carbohydrate malabsorption.

Colonization in the small intestine also results in damage to epithelial cells (cells lining the small intestine) otherwise known as leaky gut or an increase in intestinal permeability, which also impairs digestion and absorption of nutrients that can contribute even further to nutritional deficiencies, and it allows toxins, pathogens, and undigested protein molecules to enter the bloodstream that causes food sensitivities, immune reactions, inflammation, and autoimmune disorders. SIBO causes an increase in a substance called zonulin, which regulates tight junctions between our epithelial cells. High levels of zonulin weaken the tight junction between epithelial cells which contributes to leaky gut even further. Furthermore, since 70 percent of the immune system resides in or around the gut, then bacterial overgrowth can significantly impede immune function. The epithelium helps form a barrier that keeps pathogens from entering the body.

Zonulin plays the same role in the blood-brain barrier (BBB), which means an increase can cause weakening of the blood-brain barrier, leading to a leaky brain, whereby the blood-brain barrier allows substances to cross over into the brain that should not be there and contribute to brain inflammation and disruption to neurotransmitter production and function.

Like most bacteria, these bacteria prefer to feed on sugar, starches, and carbs that are present in our diet by fermenting them, which releases a variety of toxins and gases like hydrogen and methane. When these bacteria are present in an overabundance of numbers and carbs are high in the diet, then these gases and toxins can become excessive, which leads to a wide variety of symptoms like flatulence, diarrhea, bloating, cramping, indigestion, acid reflux, abdominal pain, and foul-smelling gas and/or stool, and increased or decreased motility depending on whether hydrogen or methane is produced. These gases and toxins can also damage the small and large intestine, as well as the liver, gallbladder, and stomach. All the toxins produced by bacteria may also overload the detoxification system, making it difficult for the body to eliminate naturally occurring toxins within the body from metabolism and incoming toxins from the environment, which can also result in a build-up of toxins and more degradation of mental and physical health.

With continuous access to food in the small intestine, this encourages the proliferation of the bacteria and creates a vicious cycle, whereby premature access to our nutrients leads to consumption of our nutrients, which provides them with the energy they need to multiply in numbers and continue to have access to our nutrients.

Most Common Symptoms of SIBO

The type of symptoms that are present and the severity of symptoms may vary widely from person to person depending on what species of bacteria is overgrown, the extent of overgrowth that is present, where they are located, and other conditions that may be involved. Different species have different behaviors. Overgrowth may be mild, moderate, or severe and symptoms will correspond accordingly. Some people may experience only a few symptoms that are mildly disruptive, while other people may become completely incapacitated or anything in between. Additionally, symptoms and severity of symptoms can change within the same individual on a daily basis in response to the level of overgrowth that is present at any given time. SIBO usually occurs in a gradual process; symptoms develop so slowly that one doesn’t connect all the dots until it is full-blown and they look back in retrospect.

  • Abdominal pain and cramping
  • Bloating and abdominal distension
  • Diarrhea and/or constipation. (May alternate between the two or have one or the other.)
  • Excessive gas (may smell like sulfur or ammonia)
  • Excessive belching (may also smell like sulfur)
  • Feeling full after just a few bites
  • Nausea
  • Heartburn
  • Acid reflux
  • Headaches or migraines
  • Joint and muscle pain
  • Fatigue and/or weakness
  • Steatorrhea (excess fat in stool)
  • Histamine Intolerance

However, other symptoms I have witnessed in my clients and myself include, pain in the rectum, burning on the inside near the small intestine area that may radiate to the skin on the outside, itching on the inside of the abdomen that radiates to the outside, and may even make the skin in that area turn red, gallbladder pain and problems, lots of exceptionally loud intestinal noise after eating, dry cough, stressed adrenals, dizziness, bladder pain, kidney pain, chest pain, insomnia or disrupted sleep, persistent gingivitis or periodontal disease, elevated glutamate, ringing in the ears or head, fluid and itching in the ear canal, back pain, spine and shoulder pain.

Psychological or Cognitive Symptoms Associated with SIBO

A wide variety of psychological disturbances are experienced by people with SIBO, which are often not discussed in the literature. These symptoms can be much more frightening and disruptive than the gastrointestinal symptoms. Your gut bacteria can have a profound impact on your brain in a variety of ways which manifests as cognitive or psychiatric symptoms.

When the gut lining is compromised, then toxins from the bacteria or other microbes that may reside there like Candida get into the bloodstream, once in the bloodstream, then they can travel to the brain where they may impair neurotransmitter production or function that regulates our moods, thoughts, and behavior. Additionally, bacteria may use the vagus nerve to transmit signals to the brain that may impair neurotransmitters. The vagus nerve consists of a variety of branches that travel from the brain to the gut and it is used by the brain to send messages to the gut and vice versa, and it comes in contact with the heart and other organs along the way. Signals from the vagus nerve help modulate mood, fear, and anxiety. The vagus nerve is also believed to be associated with neurogenesis (the formation of new neurons) and increasing brain-derived neurotrophic factor, a substance involved in neurogenesis and in protecting existing neurons and encouraging synapse formation.

Bacteria can also produce false neurotransmitters that would interact with neurons and they may interfere with enzymes that are needed to break down neurotransmitters. For example, the bacteria called clostridia is associated with conduct disorders, autism, depression, schizophrenia, and even psychoses by altering neurotransmitters in the brain. Certain species of Clostridia can inhibit an enzyme called dopamine beta-hydroxylase needed to convert dopamine into norepinephrine. Dr. William Shaw explains that this “results in an excess of dopamine and a deficit in norepinephrine, leading to obsessive, compulsive, stereotypical symptoms associated with dopamine and reduced exploratory behavior and learning in novel environments” associated with a norepinephrine deficit commonly seen in autistic children. Excess dopamine is also associated with schizophrenia and psychosis. These disorders often respond favorably to treatment with the antibiotic vancomycin, which targets clostridia.

Furthermore, a phenomenon called molecular mimicry may occur. For example, Rheumatic Fever is a condition that develops after an infection with a group A streptococcus bacteria, because proteins in the cell wall of the bacteria are similar to proteins that exist in various places throughout the body like the heart, brain, and joints. The immune system mistakes human tissue for the bacteria protein and attacks them. Inflammation and damage to these tissues can then lead to heart disease, arthritis, and/or abnormal movements called Sydenham’s Chorea or St. Vitus Dance. Another disorder called PANDAS, which develops in children after an infection with streptococcus, manifests as obsessive-compulsive disorder (OCD), behaviors, or tic disorders. So it is believed that PANDAS develops in a similar manner as Rheumatic Fever develops, the immune system is attacking tissue in the brain, which causes inflammation and affects the way the brain functions.

Additionally, one of the byproducts produced by some species of bacteria (predominantly gram-negative anaerobes like Enterobacteriaceae, Proteus, and Clostridium species) when they utilize protein, is ammonia. Ammonia is a neurotoxin when in excess and can lead to, neuroinflammation, impairment of neurons, brain fog, mental confusion, impaired cognitive functioning, hepatic encephalopathy, and more. High levels of ammonia deplete alpha-ketoglutaric acid, which is needed to detox ammonia out of our central nervous system, which then allows ammonia to build up to toxic levels. High levels of ammonia can overload the liver and kidneys as well and may produce a wide range of other symptoms like headaches, irritability, fatigue, diarrhea, and nausea. Utilizing protein can also lead to protein deficiencies and compromise the immune system even more.

Some bacteria produce histamine out of the amino acid histidine in the diet, which can cause an elevation of histamine. High histamine can lead to a wide variety of psychological disturbances like OCD, addiction, abnormal fears, brain racing, schizophrenia, and more, as well as physical symptoms like hives, itching, weepy eyes, runny nose, gastrointestinal symptoms, and more.

If overgrowth involves D-Lactate producing bacteria, they may cause elevated levels of D-Lactate, which is neurotoxic and may lead to neurological symptoms like brain fog, disorientation, anxiety, obsessive-compulsive disorders, depression, confusion, and more.

Dr. Emeran Mayer, a professor of medicine and psychiatry at the University of California, Los Angeles, found that connections between regions of the brain differ depending on what species of bacteria is dominant in a person’s gastrointestinal tract. Mayer states that this suggests that “what kind of brains we have — how our brain circuits develop and how they’re wired.” may be partly determined by the particular microbes that are present in our gut.

Researchers at McMaster University in Hamilton, Ontario discovered that if they replaced the gut bacteria from mice that were fearless into mice that were anxious then the anxious mice become less anxious and more gregarious and if they replaced the but bacteria of the fearless mice with the bacteria from the anxious mice, then the fearless mice became more timid. Additionally, aggressive mice would become calm when their gut bacteria was altered with diet, probiotics, and antibiotics. While researchers in Ireland found if they cut the vagus nerve in mice, then the brain would no longer respond to changes in the gut biome.

Dr. Mark Lyte of the Texas Tech University Health Sciences Center in Abilene studies how microbes affect the endocrine system and he has been quoted as saying, “I’m actually seeing new neurochemicals that have not been described before being produced by certain bacteria. These bacteria are, in effect, mind-altering microorganisms.” Athena Aktipis, Ph.D., evolutionary biologist and psychologist with the Arizona State University Department of Psychology explains that “Microbes have the capacity to manipulate behavior and mood through altering the neural signals in the vagus nerve, changing taste receptors, producing toxins to make us feel bad, and releasing chemical rewards to make us feel good.”

Since we know bacteria can have this impact on the brain, it is logical to assume that bacteria involved with SIBO would have the same capabilities. Furthermore, if SIBO has lead to nutritional deficiencies like B12, iron, calcium, and magnesium, this can also lead to a wide variety of psychiatric symptoms as the nutrients are vital for proper brain function and neurotransmitters that moderate our thoughts, mood, and behavior.

Some of the most common symptoms experienced in the brain by people with small intestinal bacterial overgrowth include, but are not limited to:

  • Brain fog (can be quite severe)
  • Obsessive Compulsive Disorder (many people with SIBO have OCD or OCD tendencies.)
  • Attention deficit
  • Hyperactivity
  • Depression
  • Anxiety
  • Impaired memory and problem solving abilities
  • Unexplained fear or paranoia
  • Thought process being choppy instead of smooth
  • Tourettes or Tics
  • Dyslexia
  • Loss of overall feelings of well-being
  • Songs or phrases getting stuck in head, but not in a normal or pleasant way.

When SIBO is more severe it may produce the following:

  • Weight loss (can be severe)
  • Malabsorption
  • Malnutrition/ Nutritional deficiencies (with iron and B12 being most common)
  • Anemia (duet to B12 deficiency or low iron)
  • Failure to thrive
  • Hepatic encephalopathy
  • (Possibly severe mental health issues like schizophrenia, psychoses etc.)

Conditions Often Associated with SIBO

One of the most common conditions associated with SIBO is irritable bowel syndrome (IBS). As a matter of fact, studies have found that SIBO is involved in more than half of all cases of IBS and in one study it was 84 percent. Successful elimination of bacterial overgrowth in the small intestine leads to a 75% reduction in IBS symptoms. In another study, even a higher percentage of people with Fibromyalgia tested positive for small intestinal bacterial overgrowth.

SIBO can also be a major underlying cause of acid reflux, heartburn, and full-blown GERD. Dr. Norm Robillard has presented a strong case in his book, Fast Track Digestion: Heartburn, that demonstrates how back pressure from gas produced by bacteria puts pressure on the lower esophageal sphincter (LES), (a muscular one-way valve at the bottom of the esophagus, which allows food to pass into the stomach but typically keeps contents in the stomach from entering the esophagus,) to open up and let the stomach acid into the esophagus. The more bacteria present in the small intestine, the more gas produced. The more gas produced, the more pressure will be exerted. Fewer bacteria equals less gas and the LES can hold firm. Other practitioners like Dr. Michael Eades support this stance as well. Dr. Eades also explains that LES gets weaker to some degree as we age, which would make it more vulnerable to gas pressure. H. pylori is also a bacteria that is implicated in the cause of GERD, but interestingly enough, H. pylori can proliferate by feeding on the hydrogen that is produced by bacteria, so it could be involved from this angle as well.

Intestinal permeability (leaky gut), when combined with a genetic predisposition and an antigen or environmental trigger, is believed to be one of the primary underlying contributors to autoimmune disorders of all kinds. When the gut lining is damaged and food, bacteria, and toxins are permitted into the bloodstream, then the immune system launches an attack against these substances. Wherever these substances land, then the immune system may target that particular organ or tissue. Since SIBO does significant damage to the gut lining, it can play a major role in the development of autoimmune disorders.

Other conditions include, but are not limited to:

  • rosacea
  • hypothyroidism
  • lactose intolerance
  • fructose malabsorption
  • chronic pancreatitis
  • hypoglycemia or low blood sugar issues
  • chronic pain syndromes
  • hepatic encephalopathy
  • interstitial cystitis
  • restless leg syndrome
  • acne
  • nonalcoholic steatohepatitis (liver inflammation from fat buildup)
  • Crohn’s
  • celiac’s
  • systemic sclerosis
  • chronic fatigue syndrome
  • diabetes with autonomic neuropathy
  • B12 deficiency
  • gallbladder problems
  • spastic colon
  • osteoporosis

Causes of SIBO

The causes of SIBO are not completely understood, but it is believed to be a complex interplay of a variety of factors. There are several protective mechanisms in the body that typically prevent SIBO from happening which include:

1. Adequate small intestine motility by way of the migrating motor complex (MMC), because lack of motility promotes bacterial overgrowth. The migrating motor complex is a process that occurs in the gastrointestinal tract whereby it triggers a wave-like action (peristaltic) that moves indigestible substances like fiber or other foreign bodies and bacteria out of the stomach and small intestine and into the large intestine. A sweeping action flows through the stomach, small bowel, and the ileocecal valve, pushing the bacteria and substances into the colon and helps keep it from re-entering. When functioning adequately, this cleansing process occurs every 90 to 120 minutes during fasting (in between meals and overnight). When food enters the digestive system, this process is inactivated and digestive motility takes over. It is believed MMC is regulated in part by serotonin and a polypeptide hormone called motilin, which itself is initiated by vagal nerve stimulation. Therefore problems with MMC could be related to serotonin insufficiency or problems with under-activity of the vagus nerve. Additionally, bile is needed to stimulate the MMC, so insufficient bile production could be a contributing factor.

2. Proper functioning of the ileocecal valve. The ileocecal valve is positioned between the ileum, (the end of the small intestine); and the cecum, which is a pouch at the beginning of the large intestine, which prevents bacteria in the colon from entering the small intestine. Put more simply, it connects the small intestine to the large intestine and prevents backflow. If the valve does not shut properly, it can allow bacteria to cross over into the small intestine. If parasites or Candida are present in the colon, and the ileocecal valve is not functioning properly, it can allow them to pass over as well.

3. Sufficient production of gastric (HCL), pancreatic (enzymes), and gallbladder (bile) secretions, because each of these helps kill bacteria.

4. Insufficient immunoglobulins in the intestinal fluid which would fight off bacteria.

5. Both heavy and moderate alcohol use is a significant risk factor for SIBO, with moderate being defined as one drink per day for women and 2 drinks per day for men. Alcohol may feed some species of bacteria, which contributes to overgrowth. It also damages the gut lining, which can contribute to leaky gut, and decreases muscular contractions. Alcohol also feeds Candida, which confounds the problem.

6. The use of proton pump inhibitors also puts one at high risk as well since they reduce the acidity of the gastrointestinal tract, which allows bacteria to multiply. Damage to nerves in the gut, opiate addiction, bowel surgery, diabetes, hypothyroidism, or any condition that affects gut motility, anatomical abnormalities like diverticula, and pancreatitis are just some of the other possible risk factors for SIBO.

7. The experts are not listing Candida overgrowth as a primary cause of SIBO, but I believe it could be a major contributing factor for the following reasons: Candida produces a toxin called acetaldehyde, which interacts with serotonin and dopamine and creates a very powerful opiate called Tetrahydroisoquinolines. Opiates inhibit the migrating motor complex and gut motility overall. Candida creates inflammation in the gut lining, which would then encourage the proliferation of pathogenic bacteria. Acetaldehyde can also deplete Acetyl Coenzyme A, which is needed to combine with choline to make the neurotransmitter acetylcholine, which can result in a deficiency of acetylcholine. Acetylcholine is used by the vagus nerve, which is needed to initiate the migrating motor complex.

Serotonin is also needed for modulating the migrating motor complex and Candida also causes serotonin depletion. Candida increases histamine release, which can then keep the body in sympathetic stress mode, which will inhibit the migrating motor complex. Candida disrupts the proper functioning of the thyroid gland, and low thyroid function can inhibit gut motility. Candida releases ammonia which lowers the pH of the gut and a low pH inhibits migrating motor complex and encourages the overgrowth of bacteria. Candida also weakens the immune system, which could decrease immunoglobulins that fight off bacteria, and it may cause irritation to the ileocecal valve, which could affect the way it functions.

SIBO can certainly occur without Candida overgrowth, but I would just like to call your attention to the fact that having Candida overgrowth increases your risk of developing small intestinal bacterial overgrowth at some point. On the other hand, all the havoc that SIBO inflicts on the body could also make one more vulnerable to Candida overgrowth. Small intestinal bacterial overgrowth also damages the gut lining, can increase ammonia levels, alter pH, irritates the ileocecal valve, and weaken the immune system, which would create an environment that encourages the proliferation of Candida. If both are present, they will perpetuate one another and an antifungal may do little good if an antimicrobial is not used as well and vice versa.

H. pylori could potentially precipitate overgrowth of bacteria in the small bowel as well; if it colonizes the stomach it reduces hydrochloric acid levels, which can then allow other bacteria to overgrowth. If it colonizes the small intestine, then it can create inflammation that encourages the overgrowth of bacteria. Additionally, as we age, our ability to produce stomach acid decreases, so aging makes all of us vulnerable to microbes of all kinds. On the other hand, the hydrogen produced by SIBO can make H. pylori proliferate, because it uses hydrogen as a food source.

8. Chronic or acute stress may also be a significant trigger or perpetuator of SIBO. When we are under stress, gastric emptying does not occur, motility is impaired, stomach acid and digestive enzymes are inhibited, healthy bacteria are killed off, immune function is impaired, communication between the brain and the gut via the vagus nerve is disrupted, nutrient absorption is impeded, the bloodstream is infused with glucose, our nutrient supply is drained to deal with the situation at hand, and inhibitory neurotransmitters like serotonin are suppressed, all situations that will encourage the overgrowth of bacteria and other microbes like Candida and H pylori.

The vagus nerve, which we mentioned earlier, is how the gut and brain communicate with one another and it is deactivated when we are under stress. The vagus nerve is also the commander in chief of the parasympathetic nervous system, which controls digestion and our relaxation response. The parasympathetic nervous system is part of the autonomic nervous system, which regulates all aspects of the body that occur automatically like digestion, breathing, heart rate, blood pressure, body temperature, sexual response, and other processes, and so is the sympathetic nervous system.

The sympathetic nervous system is activated when we are under stress. After a stressful event, the vagus nerve activates the parasympathetic nervous system to return the body back to the normal mode of rest, digest, and relaxation. The two systems work together to assure that that the body responds to different situations in the appropriate manner and has different effects on the same organ. For example, the sympathetic nervous system will increase heart rate and blood pressure, while the parasympathetic will decrease them both. The sympathetic nervous system will slow down digestion, while the parasympathetic will stimulate it. The parasympathetic nervous system also controls contractions that move food throughout the gastrointestinal tract from stomach to colon.

Stress hormones prevent the vagus nerve from turning on the relaxation response. If stress is ongoing, then the sympathetic nervous system will remain in overdrive, and communication between the gut and brain will be disrupted. The migrating motor complex is partly regulated by motilin, which is initiated by the vagus nerve. Therefore, stress will inhibit the migrating motor complex as well.

Studies show that severe stress or trauma early in life, like childhood abuse, neglect, or loss of the primary caregiver, makes the individual highly susceptible to developing functional gut disorders like SIBO or Candida overgrowth later in life. Acute, life-threatening events in adulthood like rape, a car accident, a natural disaster, being present in a war zone, can also significantly increase vulnerability to functional gastrointestinal disorders. Both acute life-threatening episodes and early life stress or trauma have the ability to cause permanent and irreversible damage to the stress response system in genetically susceptible people, whereby stress circuits remain in a hypersensitive state, keeping one in a perpetual state of stress, that can lead to functional gut disorders (and mental health issues) later in life. High levels of day-to-day stress or chronic stress can lead to or perpetuate the gut disorder and exacerbate symptoms. Furthermore, overgrowth of bacteria or any other microbe like Candida is a form of stress and thus can create a vicious circle, where overgrowth causes stress that creates conditions that encourage more overgrowth, which causes more stress and so on and so forth.

Autonomic nervous system dysfunction that leads to sympathetic dominance can also be caused by a wide variety of other factors like neurotransmitter depletion, hormone imbalance, environmental toxins, too much exercise, electromagnetic fields, physical trauma, and more.

Hydrogen or Methane Producing SIBO

Now, according to Chris Kresser, M.S. L.Ac, bacteria is not always the only organism involved in SIBO. As you may know, one of the most common tests used for diagnosing overgrowth of bacteria in the small bowel is a breath test, which measures one’s level of hydrogen and methane, two byproducts of microbe metabolism that indicate bacterial overgrowth is present. However, hydrogen is produced by bacteria, but methane is actually produced by an ancient single-celled organism called archaea.

Archaea were once believed to be a type of bacteria, but now it is understood they are a different type of organism called prokaryotes. Archaea live in extreme environments like salt lakes and hot springs or any other habitat where biodegradation of organic compounds takes place like the gut of the human being or an animal. Bacteria produce hydrogen when they ferment fiber in your diet, but archaea produce methane by consuming the hydrogen that the bacteria produce; the methane is a byproduct of this process. So this is one of the ways that the body deals with excess hydrogen. Bacteria may also convert excess hydrogen into sulfites, (hydrogen sulfide) which is one of the reasons that the breath, gas, or stool may smell like sulfur when one has SIBO. High levels of hydrogen sulfide may inhibit an enzyme needed for ATP production and thus impair mitochondrial function, (the furnaces in our body where energy is produced) which is believed it may be a contributor to chronic fatigue among other things.

If you have a high level of methane at baseline or after consumption of the sugar solution in the breath test, this indicates an overgrowth of the archaea. If you have a high level of hydrogen with no elevation in methane, this indicates an overgrowth of bacteria only.

Methane is an odorless, colorless, inert gas. At high levels, it creates bloating and distention and is associated with a variety of disease states. The research suggests that approximately 45 percent of individuals with bacterial overgrowth in the small intestine have methane-producing archaea and the level of methane produced is significantly higher in people with bacterial overgrowth than it is in people with fructose or lactose malabsorption issues. According to Dr. Pimental, SIBO expert, methane levels of over 3 parts per million indicate a methane producer, even if it is at baseline.

Another indicator that one is carrying methane-producing archaea is constipation, as these organisms are associated with chronic constipation. The higher the level of methane the slower the colonic transit time will be. One study found that if the breath test was positive for methane, there was a 100 percent association with constipation-predominant IBS. However, it’s important to note that constipation can be caused by other factors besides methane-producing archaea. If methane production is not elevated and constipation is present, then there is another underlying contributor. People who have inflammatory bowel diseases like Crohn’s or ulcerative colitis, which typically presents with diarrhea, have low levels of methane. On the other hand, it may be that constipation produces methane; slow transit time encouraging methane-producing archaea organisms.

It is believed that serotonin may be involved in this process. Serotonin is a neurotransmitter that is produced in the brain and the gut. It is believed one of the roles it plays in the gut is intestinal motility. Studies reveal that people with high levels of methane have lower post-meal serotonin levels than people with high levels of hydrogen. Hydrogen production is associated with diarrhea. If one is producing both hydrogen and methane, both constipation and diarrhea may present depending on the dominant gas at any given time. This explains why many people vacillate between diarrhea and constipation. Therefore IBS-C tends to indicate archaea methane producers are involved and IBS-D indicates hydrogen-producing bacteria only are involved.

Studies have also demonstrated that if you reduce methane levels then symptoms improve, thus if you have SIBO and address it from the hydrogen angle and don’t get improvement, this indicates that methane-producing archaea are present. Chris Kresser states that people with methane-producing archaea may also have a higher level of rectal hypersensitivity, which manifests as a pain in the rectum area or the feeling of urgency and a lower pH level of the colon in a stool test, and that it occurs more often in women than men. You should also note that methane production occurs in people without overgrowth of bacteria but at lower and non-pathogenic levels, from archaea in the colon. However, methane production does not begin until after the age of three and it is found in lower numbers in people under the age of 10 and not everyone produces methane, indicating that not everyone is colonized with archaea. Read Chris’s excellent article on the topic of methane and SIBO here.

So why does it matter if you are a methane or hydrogen producer with SIBO? Because it will affect how one approaches treatment to some degree. Antibiotics or herbs that are effective against hydrogen producers are not always effective against methane producers. We will discuss this aspect in more detail next week when I cover the topic of treatment.

SIBO Tests and Diagnosis

SIBO is largely underdiagnosed for a variety of reasons. First and foremost, many doctors are not trained to recognize SIBO, and people are diagnosed with GERD, IBS, autoimmune disorders, OCD, etc. instead of bacterial overgrowth. Furthermore, since many of the symptoms overlap with other microbial infections, it is frequently misdiagnosed as Candida or H. pylori, or, because it often exists simultaneously with H. pylori and Candida, all symptoms may be assumed that they are due to one of these. On the other hand, many people don’t seek help for their symptoms, because they medicate them with over-the-counter products like antacids, laxatives, etc. It is also underdiagnosed because the lab tests we have available are not always reliable.

The most common test used for diagnosing SIBO is called the hydrogen/methane breath test. You can order this test yourself by clicking the link in the previous sentence, but if you do be sure to do the proper prep. It measures the levels of methane and hydrogen present in the breath after a 24 to 48-hour prep diet (void of fermentable carbs) and an overnight fast. A fasting baseline level will be collected first. Then a non-absorbable sugar solution called lactulose is consumed and breath samples are collected every 20 minutes for the next three hours. Breath is collected by inhaling into a special vial designed for this purpose and then analyzed with a special machine called Breathtracker. Interpretation of results may vary from practitioner to practitioner, but according to Dr. Siebecker, if hydrogen or methane is elevated, it indicates small intestinal bacterial overgrowth. If methane or hydrogen is elevated at baseline (prior to consuming sugar solution) this indicates overgrowth as well. The Hydrogen test can also be used to diagnose H. pylori and carbohydrate malabsorption.

Testing may be done at a center that has the proper equipment to do so, or samples may be collected with a do-it-yourself-at-home kit and then sent to the lab for analysis. However, not all labs have the proper equipment to test for methane, so be sure the lab you use does. As we discussed previously, if methane is present, it will require a slightly different treatment strategy. It’s important that one has abstained from antibiotic use, both natural and pharmaceutical, prior to testing.

However, the hydrogen/methane breath test results in a substantial level of false negatives, meaning test results are negative when SIBO exists. This may occur for a variety of reasons. The small intestine is approximately 20 feet long and overgrowth may occur in one spot and not another. The breath test may use lactulose or glucose as the substrate for the test. Lactulose cannot be digested or absorbed by humans, only bacteria have this ability. When lactulose is consumed and bacteria eat it, then gas is produced. If an excess level of gas is produced, then it indicates overgrowth. According to Dr. Siebecker, lactulose is better at diagnosing bacteria that are in the distal end (lower) of the small intestine, where it is believed that most overgrowth occurs. However, it is less effective overall than glucose.

Glucose, on the other hand, is absorbed by both humans and bacteria. We absorb our glucose within the first three to five feet of the small intestine, therefore if high levels of gas are produced in response to glucose, it means that bacteria are present in the proximal/upper end of the small intestine. However, it also means glucose cannot diagnose bacterial overgrowth that occurs in the remaining 17 feet of the small intestine, where it is most likely to occur. If one gets a negative test result with one or the other, but symptoms indicate SIBO is present, then it seems logical to me that one should have the test done with both glucose and lactulose.  However, many practitioners feel that lactulose is the better substrate to use. To complicate things further, not all practitioners interpret the test the same. One practitioner may interpret a negative result, while another practitioner may interpret the same test as positive.

If there is delayed gastric emptying (time to move from stomach to small intestine),  one may get a false negative as well. Therefore, the hydrogen/methane breath test is not completely reliable for an accurate diagnosis, and one cannot assume they are SIBO free if their test results are negative. A false positive is also possible if one has chronic pancreatitis, rapid transit throughout the small intestine or high levels of oral bacteria. However, most problems lie within false negatives. If test results are negative, but the symptoms of small intestinal bacterial overgrowth seem apparent and other causes have been ruled out, then most physicians will just treat accordingly. If one has a positive result in response to treatment, then they know they are on the right track.

Another test that may be used in diagnosing SIBO is the organic acids test, particularly the one from Great Plains Laboratory. Although all organic acids tests can be highly beneficial for assessing underlying factors contributing to one’s health condition, it is my opinion that the Great Plains Laboratory Organic Acids Test is superior to other labs in its ability to identify not only bacteria throughout the gastrointestinal tract but Candida overgrowth as well. You can order this test yourself, by clicking the link in the previous sentence. The OAT test looks for high levels of byproducts in the urine that indicate bacteria or yeast is present. However, like any lab test, it is not foolproof either and doesn’t always identify overgrowth when it exists. As I see it, it should be done in conjunction with the breath test. The Organic Acids test also provides you with an abundance of information on other problems that may exist in the body like nutritional deficiencies, mitochondrial function, detoxification, and neurotransmitter function, so you can achieve many different goals at one time using this test.

Dr. Allison Siebecker states that other signs that indicate the presence of SIBO include the following:

1. Dramatic improvement in symptoms when you take an antibiotic.

2. Symptoms get worse when taking a probiotic (especially if it contains a prebiotic because this feeds bacteria)

3. Fiber makes constipation or other symptoms worse (soluble fiber feeds bacteria)

4. A Celiac person has little improvement with a gluten-free diet. (they replaced gluten with other starches)

5. Developing gastrointestinal problems after taking an opiate drug. (opiates slow motility and migrating motor complex)

6. Persistent low ferritin levels with no apparent cause. (however, please note, that parasites can cause this as well)

7. Pancreatitis is concealed by a gas bubble on CT scan. (bacteria makes so much gas that it is hidden)

You can listen to Dr. Siebecker discuss these key indicators in the following video.

Okay, so that’s it for this week. Read the second half of this post on the SIBO treatment, diet, and maintenance page.

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Siebecker, Allison, ND, MSOM, LAc, and Steven Sandberg-Lewis, ND, DHANP. Small Intestine Bacterial Overgrowth: Often-Ignored Cause of Irritable Bowel Syndrome. Townsend Letter February / March 2013.

Dukowicz, Andrew C., Brian E. Lacy, and Gary M. Levine. “Small Intestinal Bacterial Overgrowth: A Comprehensive Review.” Gastroenterology & Hepatology 3.2 (2007): 112–122. Print.

Bures, Jan et al. “Small Intestinal Bacterial Overgrowth Syndrome.” World Journal of Gastroenterology : WJG 16.24 (2010): 2978–2990. PMC. Web. 13 Feb. 2015.

Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012 Feb;42(1):71-8. doi: 10.1007/s12016-011-8291-x.

Kresser, Chris. SIBO: What Causes it and Why it’s so Hard to Treat

Shaw, William. Dr. Interference in Dopamine Conversion.

Shaw, William. “Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of Clostridia spp. in the gastrointestinal tract, in urine samples from patients with autism and schizophrenia” Nutritional Neuroscience. 13. (2010): 135-43. Print.)

Peter Ott, Otto Clemmesen, Fin Stolze Larsen. Cerebral metabolic disturbances in the brain during acute liver failure: From hyperammonemia to energy failure and proteolysis, Neurochemistry International, Volume 47, Issues 1–2, July 2005, Pages 13-18, ISSN 0197-0186, https://dx.d

Frederick, R. Todd. “Current Concepts in the Pathophysiology and Management of Hepatic Encephalopathy.” Gastroenterology & Hepatology 7.4 (2011): 222–233. Print.

Vince AJ, Burridge SM.Ammonia production by intestinal bacteria: the effects of lactose, lactulose, and glucose. J Med Microbiol. 1980 May;13(2):177-91.

Irena Ciećko-Michalska, Małgorzata Szczepanek, et al. “Pathogenesis of Hepatic Encephalopathy,” Gastroenterology Research and Practice, vol. 2012, Article ID 642108, 7 pages, 2012.

National Institute of Mental Health. PANDAS: Frequently Asked Questions about Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections.

Stein Rob. Gut Bacteria Might Guide The Workings Of Our Minds. November 18, 2013

Norris, Jeffrey, Do Gut Bacteria Rule Our Minds? University of California, San Francisco, August 15, 2014.

Uday C. Ghoshal, Ratnakar Shukla, Ujjala Ghoshal, et al. “The Gut Microbiota and Irritable Bowel Syndrome: Friend or Foe?,” International Journal of Inflammation, vol. 2012, Article ID 151085, 13 pages, 2012.

Pimentel M, Wallace D, Hallegua D, Chow E, Kong Y, Park S, Lin HC. A link between irritable bowel syndrome and fibromyalgia may be related to findings on lactulose breath testing. Ann Rheum Dis. 2004 Apr;63(4):450-2.

Eades, Dr. Michael, GERD: Treat it with a low or high carb diet. September 23, 2013.

Robillard, Norm. Fast Track Digestion: Heartburn. Self Health Publishing; 1 edition (October 26, 2012)

Takahashi, Toku. “Mechanism of Interdigestive Migrating Motor Complex.” Journal of Neurogastroenterology and Motility 18.3 (2012): 246–257. PMC. Web. 13 Feb. 2015.

Hauge T, Persson J, Danielsson D. Mucosal Bacterial Growth in the Upper Gastrointestinal Tract in Alcoholics (Heavy Drinkers). Digestion 1997;58:591-595

Gabbard SL, Lacy BE, Levine GM, Crowell MD. The impact of alcohol consumption and cholecystectomy on small intestinal bacterial overgrowth.
Dig Dis Sci. 2014 Mar;59(3):638-44. doi: 10.1007/s10620-013-2960-y. Epub 2013 Dec 10.

Levin, I., Meiri, G., Peretz, M., Burstein, Y. and Frolow, F. (2004), The ternary complex of Pseudomonas aeruginosa alcohol dehydrogenase with NADH and ethylene glycol. Protein Science, 13: 1547–1556. doi: 10.1110/ps.03531404

Mönnikes H, Tebbe JJ, Hildebrandt M, Arck P, Osmanoglou et. al.Role of stress in functional gastrointestinal disorders. Evidence for stress-induced alterations in gastrointestinal motility and sensitivity. Dig Dis. 2001;19(3):201-11.

Bures, Jan et al. “Small Intestinal Bacterial Overgrowth Syndrome.” World Journal of Gastroenterology : WJG 16.24 (2010): 2978–2990. PMC. Web. 13 Feb. 2015.

Carpenter Siri Dr. That gut feeling. American Psychological Association. September 2012, Vol 43, No. 8. Print version: page 50

Dix Lemle, Marian. Hypothesis Is ME CFS Caused by Dysregulation of Hydrogen Sulfide Metabolism. Journal: Med Hypotheses. 2008 Sep 15. [Epub ahead of print]

Simrén, M, and P‐O Stotzer. “Use and Abuse of Hydrogen Breath Tests.” Gut 55.3 (2006): 297–303. PMC. Web. 13 Feb. 2015.
Aglaée Jacob, MS, RD. Gut Health and Autoimmune Disease – Research Suggests Digestive Abnormalities May Be the Underlying Cause. Today’s Dietitian
Vol. 15 No. 2 P. 38 February 2013 Issue.

Grace, Liu, Dr. Don’t Take Resistant Starch If You Have Moderate to Severe Irritable Bowel Syndrome (IBS) Temporarily (Part 3) Thursday, October 2, 2014

Tana, C., Umesaki, Y., Imaoka, A., Handa, T., et. al. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterology & Motility, 22: 512–e115. doi: 10.1111/j.1365-2982.2009.01427.x

Emeran A. Mayer , Bruce D. Naliboff , et al. V. Stress and irritable bowel syndrome. American Journal of Physiology – Gastrointestinal and Liver Physiology Published 1 April 2001 Vol. 280 no. 4, G519-G524 DOI:

18 thoughts on “SIBO 101: A Comprehensive Guide to Small Intestinal Bacterial Overgrowth”

  1. Thank you Cynthia, for your comprehensive, informative and well-researched articles. I have suffered with H. pylori for years, and look forward to your upcoming articles on this topic . . diet, maintenance, and hopefully preventative measures to keep this bacteria from returning. Once again, my heartfelt thanks for your timely info! Keep up the good work !

  2. Oh my.. Incredibly Complex. Still thinking I might have this since my symptoms are mostly 1-2 hours after eating , GI docs already gave up on me not before cutting out my healthy GB first, which just about killed me, and I fit the mold the more I research SIBO. Getting tired of treating invisible illness when I don’t know what I have, except lots of pain & suffering (changes a person), and sure I’m a picture of health otherwise. Also attended healthy gut summit, I’m really sensitive, now I can see much more into the window of intestinal health, it’s manifestation upon mind, body, spirit, soul.

  3. I have many symptoms mentioned and have been told I have Candida overgrowth. I think its more than that though. I have so many new ailments including swollen joints (especially in my hands), continuous yeast infections, brain fog and more. Thank you for writing about this, I feel hopeful that I can restore my health …. somewhat.

  4. Thank you for this thorough overview. It covers pretty much everything I’ve been researching over the last several years. It makes it -slightly- less overwhelming to see it all in one place.

    Question: Rifaxamin would work in place of Vancomycin to combat clostridia + SIBO, correct?

  5. Cynthia, are you sure that if someone have sibo + clostridia he should avoid meat? You cite Norman Robillard here but In his book I don’t remember he saying anything about this problem – his main idea is fermentation potential and meat have zero fermentation potential so it should not be problem for sibo.
    I have sibo + clostridia /organic acid test show this/ and it seems to me that your version is more correct than Norman’s.
    I mean – am I missing something here or Norman’s research is not good enough?

  6. Cynthia, do you see a lot of patient suffering from panic attack and anxiety due to sibo? I started having panick attacks and severe anxiety last year from nowhere. I never had those issue in my entire life.I am seeing a Functional med dr who confirmed I have severe sibo even though I have no GI Sympthoms.

    1. Admin - Cynthia Perkins

      Hi Jenn,

      Yes, I do. Anxiety and panic attacks are very common symptoms with SIBO.

      Sometimes people with SIBO have no GI symptoms and experience it completely in their mental health.



  7. Hi Cynthia,

    I’m sure that I’ve got SIBO from all your helpful information above, but I’ll talk to the doctor about it anyway before I stare taking any medical advice. What’s the best antibiotic to combat the overgrown bacteria thinking about the last couple of years I’ve been drinking quite regularly alcoholic drinks and I’ve been diagnosed with IBS in 2014. Now I’m only drinking occasionally.
    Thank you


    Florin Fechete

  8. Hi Cynthia. I know this forum is old but I can’t find anyone else to ask. I’m 16 years old and 6 months ago I developed really bad constipation which I still have, bloating, air bubbles in water after stool, I started getting anxiety, swollen glands in my neck which are still there. And lots of other symptoms. It hurts when I push around my abdomen. Doctor said it was just ibs and anxiety as the tests I had were fine. Because I live in England the nhs don’t really provide tests for this or antibiotics. I don’t know what to do. I can’t really afford to go private as my family isn’t very wealthy and we just about get by. Anything I can do to help this? Does it sound like sibo, candida, h pylori? I don’t know what to do and I feel like I will never get better

    1. Admin - Cynthia Perkins

      Hi Dylan,

      I can’t say for sure, but sounds like SIBO. I’m sorry, I really can’t advise you what to do since you are not an adult. Educate yourself and try to find a doctor who has some knowledge. IBS and anxiety are commonly caused by SIBO or other microbial issues.



  9. Psychological or Cognitive Symptoms Associated with SIBO caught my attention. When I am in relapse I get these symptoms and depending on the severity of SIBO and/candida I get terrible anxiety, depression, fear, even paranoia at times. It is so overwhelming that I can barely handle it. I get so exhausted that I can barely function. I need help but no one seems to know what is wrong with me.

  10. Liduina Wildenburg

    Thank you for this brilliant article! I wonder which markers on the Great Planes OAT test are indicative for SIBO. I was told that high DHPPA (Beneficial Bacteria) could indicate SIBO. Other tests have shown that the beneficial bacteria don’t reside in the large intestine so that would make sense. And another question: is it possible that someone with SIBO is extremely sensitive to B vitamins (resulting in extreme anger and panic attacks)? I was told that the bacteria in the small intestine eat the vitamins and release toxins which is why someone with SIBO might feel extremely anxious after supplementing with B vitamins.

  11. I have no doubt why I developed SIBO. After a short opioid anesthesia, FENTANYl, which paralyzed my gut and there was proliferation of bacteria, I had a bowel impaction the next day after the anesthesia. (I had never even had constipation) I had onset of severe SIBO symptoms ongoing for nearly a year with a 20-pound weight loss. After suffering for nearly a year, I found the website of
    Dr. Pimentel. I have reduced symptomatology taking the recommended herbs and with diet modification but it is a lifetime “curse” which interferes with my lifestyle. Hippocrates was right, “All disease begins in the gut.”

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