Once put under the catch-all label of Irritable Bowel Syndrome (IBS), Small Intestine Bacterial Overgrowth (SIBO) is now a much better understood condition. SIBO happens when bacteria overrun the small intestine. This causes a host of chronic digestive ailments such as severe bloating, diarrhea, and/or constipation. If you experience severe bloating or diarrhea after almost every meal, this might be the cause.

Our digestive systems naturally contain an ecosystem of bacteria that aid us in breaking down our food. This is especially true of the large intestine which is designed to host large quantities of bacteria. In a healthy gut, food travels relatively quickly through the digestive tract until it hits the large intestine. Once here, food slows down and take a day or two to pass through. During this transit, bacteria feast on the incoming food and produce gas as a byproduct, which the large intestine easily handles and expels.

By contrast, the small intestine is not equipped to handle a build up of food or bacteria. While the large intestine has few curves and is about 5 feet long and 3 inches wide, the small intestine is about 20 feet long, 1 inch wide, and tightly coiled! It simply can’t handle gas production the way the large intestine can. When bacteria build up in the small intestine, bloating is intense and the abdomen expands so much it feels like it’s going to explode. Sometimes bloating is so severe it can be hard to breathe as the diaphragm gets compressed upwards. Most foods contain complex carbohydrate that release tons of gas when ingested. For someone suffering from SIBO, most foods cause extreme bloating and discomfort!

Often, not only has the small intestine become overrun with bacteria, but they are the wrong sorts of bacteria. Instead of the bacteria our bodies are adapted to work with, the ecosystem can become dominated by other micro-organisms not typically major players in human digestion.

Additionally, the lining of the small intestines can become inflamed and damaged from all of this abuse. The abdomen can become very sensitive which causes intense pain from any pressure exerted on it, for example the waistband on pants or seat-belts!


Small Intestine Fungal Overgrowth (SIFO) is very similar to SIBO, but is caused by an overabundance of yeast instead of bacteria. Yeasts normally make up an insignificant proportion of the intestinal gut fauna, but with SIFO they can dominate! The type of yeast in question is Candida, most commonly Candida albicans, though other varieties can invade as well. The foods that trigger reactions with a pure SIFO infection are different, but the resulting gastrointestinal distress is comparable. When both fungal and bacterial cultures are present, the symptoms and triggering foods can be almost identical.

SIBO can also turn into SIFO if not treated correctly! Because part of the treatment for SIBO is to use antibiotics, if probiotics are not being administered at the same time, the problematic bacteria can be wiped out just to leave a blank slate for yeast to move in. If you were diagnosed with SIBO, treated with antibiotics, and the condition did not improve or got worse, make sure your doctor checks for fungal culprits!


The effects of SIBO can range from mild to severe, depending on how far it’s progressed. Until treated, the symptoms can worsen as the health of the small intestine deteriorates. Severe forms of this condition are not going to go away of their own, so it’s important to seek help as soon as possible. Trust me, I know from experience! You do not want to suffer from this for years on end!

  • Bloating after meals
  • Diarrhea, constipation, or alternating between the two
  • Sharp stabbing pains in abdominal region
  • Sensitive abdomen, external pressure can cause pain and nausea
  • In the case of SIFO, abnormally large amounts of burping may be experienced. Additionally, symptoms common with fungal infections are more likely to manifest, such as skin rashes


Broad spectrum antibiotics

These were the panacea to cure all ills, from pneumonia to ear infections; but it turns out these antibiotics also kill the beneficial bacteria in the digestive tract. This upsets the natural balance and can leave a vacuum for other bacteria or fungi to move in.

Chronic constipation / slow system

The body is designed to move food relatively quickly through the small intestine. With chronic constipation, or a slow digestive system in general, food lingers in the small intestine instead. This creates a welcoming environment for bacteria from the large intestine to migrate up into the small intestine.

Traveler’s diarrhea or other extreme food poisoning

When traveling abroad, visitors may experience a kind of stomach flu caused by consuming products containing foreign bacteria. These microorganisms will battle with those originally present in the digestive system and cause symptoms similar to a stomach flu or food poisoning. Typically these symptoms only last a couple of days until the digestive ecosystem corrects itself. In severe cases, the digestive system can become so badly affected it degrades into a SIBO situation.


Hydrogen breath test

This test involves ingesting a sugar filled syrup and taking a breath sample every 15 minutes for 3 hours. The breath samples are analyzed for hydrogen and/or methane to determine if there is a likely overgrowth situation in the small intestine. When the bacteria eat this sugar, it will produce gas which then enters the bloodstream and is expelled when you exhale. In a healthy individual, little hydrogen or methane will be detected for the duration of the test. For someone with SIBO, these gases will spike during the test, indicating an abnormally large number of bacteria are present and eating the sugar.

Typically this test either uses the sugar lactulose or glucose. Glucose is better at indicating an overgrowth of the first couple feet of the small intestine, lactulose, the last couple feet. Many doctors only use the lactulose test, which may not indicate a problem if the overgrowth only resides in the upper portion of the small intestine. SIFO has not been studied as extensively; it may not display the same results as seen in SIBO cases.

These tests are somewhat subjective as there isn’t necessarily a hard line between high gas production and low. Doctors should keep other patient symptoms in mind when deciding a likely diagnosis. The patient reaction to the test itself provides another clue, as the sugar solution can cause a great deal of bloating and discomfort for anyone suffering from bacterial/fungal overgrowth.

Stool sample

To check for SIFO, a stool sample can be taken and analyzed for the presence of yeast and bacteria. If fungal overgrowth is detected, this also determines which Candida varieties are present which helps immensely in knowing which anti-fungal medications will work best.

Additional testing

A list of additional diagnosis methods is kept up-to-date on Dr. Allison Siebecker’s SIBO website. She is a medical professional leading the research to understand and treat this disorder:

Alleviating symptoms

While waiting for further treatment, whether you are finding a doctor or working with one to treat underlying conditions, there are things that can help improve the symptoms in the meantime. Nothing in this section is likely to fix SIBO/SIFO by itself. However, many of these remedies can help improve digestion and reduce inflammation of the intestinal tract, and for these reasons can aid in treatment.


The quickest way to alleviate symptoms is to be very careful about what you eat. When bacteria and fungi eat certain carbohydrates, they produce immense quantities of gas as a by-product. Trapped inside the small intestine, this causes immense discomfort and bloating.

It is important to note that the foods to avoid as a part of these diets are not bad foods for healthy people, and once you’ve recovered they should be added back to your diet. However, until you feel better, they are best avoided to allow your gut to heal and to limit painful symptoms.

In addition to the foods listed under the SIBO and SIFO categories below, an inflamed intestine may also be sensitive to foods that further irritate the gut. Spicy foods like hot peppers and rough foods such as nuts, uncooked vegetables, and uncooked fruits can further inflame the intestinal lining and cause pain. These foods are not eaten by bacteria or fungi, but may need to be avoided by sensitive individuals until the gut has time to heal.


The foods that release the most gas when digested contain high amounts of complex carbohydrates called FODMAPs, Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. These complex carbohydrates are mostly found in plant based foods. Animal based products are devoid of these compounds with one notable exception: lactose. Two of the most potent sources of FODMAPs are also the hardest to eliminate: garlic and onions. Just avoiding these makes this diet very hard to follow. After all, almost every savory dish prepared contains onions. That said, this diet is probably the best for relief from bloating.

Dr. Allison Siebecker has an extensive list of dietary recommendations for those suffering from SIBO. When I had SIBO/SIFO, I followed her SIBO Specific Food Guide which includes the Low FODMAP diet as part of it. This diet helped me immensely with the reduction of bloating, abdominal sensitivity, and pain.


Candida feeds on sugar. The one sugar that causes immense bloating when broken down is lactose, the sugar found in milk. While consuming other sugars will not cause severe bloating, they still exacerbate SIFO and can cause other gastrointestinal issues such as diarrhea, constipation, pain, minor bloating, and a weakened immune system.

Fresh whole fruits are the easiest sugar to tolerate, especially if eaten alongside fat and protein, but for many, even fruit can be hard to handle. Fructose can be harder to handle than glucose, so high-fructose fruits may need to be avoided.

Some individuals are so sensitive that even starches, especially refined starches, are poorly tolerated. The gut breaks down starches into simpler sugars which the yeast can then eat.

The following is a list foods and how well they are tolerated by those suffering from SIFO, ordered from the easiest to handle to the worst. Use the list as a guide, alongside your experience with these foods, to determine what you can tolerate:

  • Foods with no starches or sugars will not cause reactions from SIFO. These include: meat, fish, eggs, fats, low-sugar low-starch vegetables, lactose-free dairy (follow the link for an explanation, lactose-free may not mean what you think). Note that sugar is sometimes added to otherwise sugar-free foods like bacon and mayo. The very sensitive may need to avoid anything with added sugar, even if it’s a small amount.
  • Low-starch foods, such as nuts and beans, are generally tolerated well.
  • Low-sugar foods are also generally tolerated well. This list includes sweet vegetables such as carrots, green peas, sweet corn, tomatoes, and winter squash (pumpkins).
  • Whole grains and other unrefined starch sources are often handled well. The fiber found in unrefined starch sources slows how fast the body can break the starch down into simple sugars. This aids in preventing a glut of sugar from being released in the digestive tract at once, feeding the yeast. Examples include: whole grains and whole grain flours; starchy fruits and vegetables such as potatoes, sweet potatoes, taro root, plantains, and jack fruit.
  • Refined starches are sometimes tolerated and include white flour, white/polished rice, corn starch, potato starch, tapioca flour, and arrowroot flour.
  • Fresh whole fruits are sometimes tolerated. Low-fructose, high fiber, and lower sugar fruits may be easier to tolerate. The following table provides carbohydrate information for a large variety of fruits along with an approximate score (lower = better tolerated) to give an idea of how easy each may be to handle:

Fruit Sugar Content

Fruit Glucose Fructose Sucrose Starch Fiber Fructose Surplus Total Sugars Score
Cranberries 3.44 0.67 0.16 0 3.6 -2.77 4.27 0.6
Pomegranate 7.8 5.7 0 0 6.4 -2.10 13.50 1.6
Passion-fruit 2.3 1.9 1.5 0 13.9 -0.40 5.70 2.7
Apricots 2.37 0.94 5.87 0 2 -1.43 9.18 3.1
Plum 5.07 3.07 1.57 0 1.4 -2.00 9.71 3.3
Fig 4.2 3.9 0 0 3.3 -0.30 8.10 3.5
Cherries 6.59 5.37 0.15 0 2.1 -1.22 12.11 3.7
Raspberries 1.86 2.35 0.20 0 6.5 0.49 4.41 3.7
Guava 1.1 2 0.3 0.1 5.4 0.90 3.40 4.1
Papaya 4.09 3.73 0.00 0 1.7 -0.36 7.82 4.2
Strawberries 1.99 2.44 0.47 0.04 2 0.45 4.90 4.3
Persimmon 5.44 5.56 1.54 0 3.6 0.12 12.54 4.3
Nectarine 1.57 1.37 4.87 0.07 1.7 -0.20 7.81 4.3
Peach 1.95 1.53 4.76 0 1.5 -0.42 8.24 4.4
Lime 0.60 0.61 0.48 0 0.4 0.01 1.69 4.4
Banana 4.98 4.85 2.39 5.38 2.6 -0.13 12.22 4.4
Blueberries 4.88 4.97 0.11 0.03 2.4 0.09 9.96 4.5
Orange 1.97 2.25 4.28 0 2.2 0.28 8.50 4.6
Kiwi 4.1 4.7 0 0 3 0.60 8.80 4.6
Grapefruit 1.61 1.77 3.51 0 1.6 0.16 6.89 4.6
Pineapple 1.73 2.12 5.99 0 1.4 0.39 9.84 5.7
Lemon 0.99 1.10 0.43 0 0.3 0.11 2.52 5.9
Cantaloupe 1.54 1.87 4.35 0.03 0.9 0.33 7.76 6.2
Pears 2.6 6.42 0.71 0 3.1 3.82 9.73 7.9
Apples 2.43 5.9 2.07 0.05 2.4 3.47 10.40 7.9
Mangos 2.01 4.68 6.97 0 1.6 2.67 13.66 8.5
Grapes 7.2 8.13 0.15 0 0.9 0.93 15.48 9.7
  • Fruit juice is not generally well tolerated unless it’s from very low-sugar fruits such as unsweetened pure cranberry juice or lemon/lime juice.
  • Unrefined sugar in very small amounts, 1/4 tsp in a single prepared meal for example, may be tolerated
  • Refined sugar, again, this may be tolerated in very small amounts
  • Dried fruit is not often handled well. The only dried fruit that might be tolerated, due to it’s extremely low sugar content, is unsweetened dried cranberries; as in, not even sweetened with apple juice.

Aiding poor overall digestion

If your whole digestive system is shot, your body will have difficulty breaking down and absorbing nutrients by itself. This is further complicated when it has to compete against an overgrowth of bacteria and/or yeast in the small intestine.

  • Wait 4-5 hours between meals – Between meals don’t eat or drink anything but water. Small amounts of tea and coffee are also permitted if plain, no milk or sugar. This allows the small intestine to flush out food, which helps prevent food from sitting in the gut feeding the overgrowth.
  • Chew your food – Food is first broken down in your mouth with your teeth and saliva. If you gulp your food down, you miss out on this extra aid.
  • Digestive enzymes – These help the body break down food, especially if it’s not producing enough on its own.
  • Bile salts – If your body is not producing enough bile, it will have a difficult time breaking down fats
  • HCL (Hydrochloric Acid) – This is the acid normally produced in the stomach, needed to break down food. If your body isn’t producing enough it hampers the whole digestive pipeline. HCL is an acid and dangerous if taken incorrectly. Consult with your physician first!
  • Apple cider vinegar – Useful if your stomach acid is low and does not carry the risks HCL does


This is not a ailment that can be easily overcome by yourself. You need to work with a doctor! They don’t have to be a specialist, and in fact, I can’t recommend going to a gastroenterologist at a large practice. It seems like the intuitive choice, as they do have extensive knowledge of GI disorders after all. However, it’s hard to find a doctor at one of these clinics that can commit the time to fully treat this condition. These clinics do not prioritize patient-doctor time and unless your case happens to be an easy fix, these doctors may shove you out the door when you don’t immediately respond to treatment!

Search for a good doctor, preferably one who is familiar with SIBO. Since treatment can be a complicated process, it’s not always as simple as taking a pill, make sure you have a very supportive doctor who will see your treatment through to the end! Often, there are underlying conditions that need to be addressed, if not to help treat the overgrowth, then at least to prevent a relapse.

Though much less well known than SIBO, SIFO requires an entirely different treatment plan. Treating a fungal infection with antibiotics, the method used to treat SIBO, will worsen SIFO since the competing bacteria will be killed off. This makes it imperative for your doctor to make a correct diagnosis before beginning treatment!

A full treatment plan has three phases:

  1. Treat any underlying conditions
  2. Reset the digestive ecosystem with antibiotics and/or anti-fungals, depending on the diagnosis, while also reintroducing beneficial bacteria
  3. Lifestyle changes to prevent a relapse

Fix underlying conditions

Have your doctor run a blood workup to check for additional problems. For example, constipation and slow digestion can be exacerbated by hypothyroidism and other conditions that should be stabilized first. In addition, improving your overall health can do wonders to speeding up a sluggish system and giving the body the energy it needs to fight off invaders.

If constipation is present, it needs to be addressed before further treatment. Issues such as food allergies can be an underlying cause for constipation, so it’s a good idea to have your doctor run tests. In the short term, magnesium is one of the best remedies as it both speeds up the transit of food and the human body needs it for energy production. Magnesium is sold in different forms. While magnesium oxide is the easiest to find in stores, it is also the least effective. The best forms are magnesium chloride or magnesium citrate.

The benefits of eating a Low FODMAP diet during treatment has been debated. Certainly, this diet helps many reduce the intensity of symptoms. The complex carbohydrates present in FODMAP containing foods feeds bacteria, both good and bad. Some doctors recommend eating FODMAP containing foods during treatment to feed the probiotics. Others caution against it because it feeds the problematic bacteria and can further inflame the small intestine. During my treatment, I stayed on a Low FODMAP diet, as I was incredibly sensitive to higher FODMAP foods, and the treatment was a success.

Resetting the ecosystem

This is the linchpin to fixing SIBO and SIFO. It’s the nuclear option. The point is to wipe out the whole digestive ecosystem and start over. This part of treatment should not be taken lightly. It should only be attempted under the supervision of a good doctor. Things can still go wrong, potentially even leaving you in a worse state than before, but a good doctor will continue to help get things back on track.

During this phase, sugar and lactose should be eliminated from the diet. These sugars feed yeast. Eating them can encourage a transition from SIBO to SIFO during treatment or, if SIFO is already present, will inhibit its cure. For those not suffering from a Candida infection, whole fruits are the one exception and may be fine to eat. They release sugar more slowly, giving the body a much better chance to absorb it before yeasts do.


First, the bacteria from the small intestine are cleared out using powerful antibiotics. This phase of treatment generally lasts 1-4 weeks depending on the strength of the antibiotics. Despite the fact that the intent may be to only clear out the small intestine, it will kill bacteria along the whole pipeline, good and bad.

The antibiotic treatment must be immediately followed with probiotics to replenish the digestive tract with beneficial bacteria. The two ways to get probiotics are from pills containing specific strains of bacteria or from consuming cultured/fermented foods as a part of your diet. Your best bet may be to use both sources.


Fungal overgrowth is slightly more complicated to treat than bacterial growth. The different varieties of yeast require different treatments, so determining the strains that dominate your system helps determine the best anti-fungal medications to use.

In addition, Candida is much better at protecting itself from harmful substances, like anti-fungal medications. It coats itself in a protective medium and clings to the walls of the small intestine. Thus, in addition to anti-fungals, medication known as a bio-film buster is often also needed to flush yeast from the sytsem. It may also be necessary to follow a strict low-carb diet for the duration of the anti-fungal treatment to completely eradicate SIFO.

Anti-fungal treatment can be brutal. When the Candida dies, known as a die-off reaction, your digestive tract is flooded with dead fungi and toxins. While your body is dealing with the fall out, your may experience adverse symptoms such as nausea, brain fog, and flu-like symptoms. For this reason, the general advice is to start with a lower dose of anti-fungal medication and work your way up. Don’t worry though, the first few days are the worst and the symptoms from die-off dramatically ease up as the yeast population drops.

Probiotics should be consumed during and after the anti-fungal and bio-film buster treatment. Just as with SIBO, probiotics can come in the form of pills or cultured/fermented foods.

Food reintroduction

Once SIBO/SIFO has been treated, slowly try to reintroduce problem foods that were avoided while suffering from overgrowth. It can take a while before foods are completely tolerated again. If you continue to have trouble with something, try eating it in a fermented/cultured form. Not only will it be easier to handle this way, as some of the complex carbohydrates are broken down during fermentation, but it might even reintroduce the beneficial bacteria you need to eat it!

Reintroduction via fermented vegetables seemed to help me, though this might be a total coincidence. When I first tried to reintroduce mushrooms, they still caused too much bloating for comfort. So, I made pickled mushrooms, using fermentation, not vinegar. The pickled mushrooms were much easier to handle. A couple of weeks later I tried straight up cooked mushrooms again and found that the bloating was minimal. Maybe eating the fermented version helped, maybe it didn’t change anything. This can be something to try at least!

Preventing a relapse

  • Improve health in general and address underlying conditions like a slow digestive tract
  • Prevent constipation if this was an issue
  • Incorporate cultured and fermented foods into your diet. These will constantly replenish the beneficial bacteria in your gut, giving you more resilience against future upsets.

Parting words

Despite some claims that SIBO can be remedied with diet alone, I don’t think that’s true for most people. In any case, the faster your gut is returned to normal the better, and the quickest way to do that is to work with a doctor. Additionally, there are real problems that result from eating a heavily modified diet long-term.

When I suffered from SIFO, testing showed the yeast strain I was suffering from to be Candida krusei, a less common fungal invader. One of the powerful anti-fungals for this yeast happens to be garlic, something I had been avoiding in my diet. Garlic is a very high FODMAP food, so eating it would cause me an immense amount of bloating and pain. After starting other targeted anti-fungal medications, ones without garlic, my reaction to problem foods finally started to improve. At this point I added a tiny amount of garlic into my diet, just 1/8 of a teaspoon. Even that caused me bloating, though it was finally tolerable, barely. Once garlic was back in the diet, the yeast beat a hasty retreat and I was well on the road to recovering from SIFO. This just goes to show the power foods play in the make-up of our digestive ecosystem, and how staying on a Low FODMAP diet long-term can worsen the ecology of the gut.

Don’t spend your days in agony while your condition gets worse. Find a doctor who will work with you to beat this. My treatment was a long and winding road, but ultimately I was healed, you can be too!

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What meds or supplements have you used for treating sifo?