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SIBO Foods: Preventing small intestinal bacterial overgrowth relapse through diet

Small intestinal bacterial overgrowth is a condition where too many bacteria live in the small intestine. Doctors can treat this overgrowth, but the bacteria often return. Studies show that up to 44 percent of people get the condition again within nine months of their first treatment¹. Food is the main way to stop these bacteria from coming back.
The small intestine absorbs nutrients from food. When too many bacteria live there, they eat the food before the human body can absorb it⁴. The bacteria eat carbohydrates and produce gases. These gases cause bloating, pain, and changes in bathroom habits⁵. Preventing a relapse means eating foods that starve the bacteria while feeding the human body.

The migrating motor complex

The small intestine has an automatic cleaning system called the migrating motor complex⁷. This system uses muscle contractions to sweep through the stomach and the small intestine. It is like a street sweeper⁷. It pushes leftover food, dead cells, and bacteria down into the large intestine⁸. This sweeping motion keeps the bacteria from crawling backward into the small intestine⁷.
The cleaning wave happens in a cycle that takes 90 to 120 minutes⁷. The cycle has four parts. Phase one is a resting period. Phase two involves weak, irregular muscle contractions. Phase three is a strong burst of rhythmic contractions that lasts for five to ten minutes. Phase four is a short transition back to rest⁷.
This cleaning cycle only happens when the stomach is empty. Eating food stops the migrating motor complex completely⁸. The cleaning wave pauses for about 90 to 120 minutes after a person eats⁸. If a person eats snacks all day, the strong phase three contractions never happen. Without this cleaning wave, bacteria build up in the small intestine and cause a relapse³.
Stress also stops the cleaning wave. High stress levels shut down the muscle contractions, causing bacteria to stay in the small intestine⁹.

Meal spacing

Because the cleaning wave needs an empty stomach, doctors recommend leaving four to five hours between every meal⁵. During this time, a person eats no food. They can only drink water, black coffee, or plain herbal tea⁵. These drinks do not trigger the digestive hormones that stop the cleaning wave.
Spacing meals gives the digestive system enough time to clear out food from one meal before the next meal arrives⁵. This keeps fermentable food from sitting in the small intestine.
Fasting overnight is another rule for preventing a relapse. The migrating motor complex is very active while a person sleeps. People are advised to stop eating at least two hours before going to sleep³. A 12-hour fast overnight gives the small intestine time to run several uninterrupted cleaning cycles before breakfast⁸.

How bacteria eat and produce gas

Gut bacteria eat carbohydrates. The human digestive system uses enzymes to break down food. Bacteria break down food through a process called fermentation⁵.
When bacteria ferment carbohydrates, they make gas. Depending on the exact type of bacteria in the gut, this fermentation makes hydrogen, methane, or hydrogen sulfide gas⁵. Hydrogen gas causes diarrhea⁶. Methane gas causes constipation and slows down the digestive tract⁶. Hydrogen sulfide gas also causes diarrhea⁶. These gases stretch the small intestine and cause pain⁵.
Bacteria do not ferment proteins or fats⁴. They need carbohydrates to survive. However, bacteria prefer complex carbohydrates and specific sugars that the human body cannot digest easily⁵. To prevent a relapse, a person eats carbohydrates that the human body absorbs very quickly. If the human body absorbs the food high up in the digestive tract, no food reaches the bacteria living lower down in the small intestine¹².

Dietary plans for relapse prevention

There are a few structured diets that help prevent small intestinal bacterial overgrowth from returning.
Dr. Mark Pimentel and researchers at Cedars-Sinai Medical Center developed the low fermentation eating plan¹¹. This diet reduces fermentable carbohydrates but allows a wide variety of foods¹¹. The main rule is to eat simple, easy-to-digest carbohydrates and avoid complex fibers⁵. Foods like white rice, potatoes, and white bread are allowed¹¹. The human body breaks down these simple starches fast. They absorb into the bloodstream before they reach the bacteria¹². The diet limits whole grains and tough vegetables⁵. The human body cannot digest high-fiber foods. They pass through the stomach intact and feed the bacteria⁵.
Monash University created the low FODMAP diet¹¹. FODMAP is an acronym for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols¹⁶. These are short-chain carbohydrates that the human small intestine absorbs poorly¹⁶.
Oligosaccharides are fibers found in wheat, rye, garlic, onions, and beans¹⁶. The human body has no enzymes to break them down. Disaccharides refer mainly to lactose, the sugar in cow’s milk. If a person does not have the lactase enzyme, lactose ferments in the gut⁴. Monosaccharides refer to fructose. Excess fructose is found in honey, apples, and pears¹⁶. Polyols are sugar alcohols like sorbitol and xylitol. They are found in certain fruits, mushrooms, and artificial sweeteners¹⁶. Sugar alcohols pull water into the intestines and ferment easily.
The low FODMAP diet is a temporary process with three parts. These parts are elimination, reintroduction, and personalization⁵. In the elimination phase, a person stops eating all high-FODMAP foods for two to six weeks¹³. This starves the bacteria. In the reintroduction phase, the person tests one specific FODMAP group at a time to see if symptoms return¹¹. In the personalization phase, the person builds a long-term diet that only excludes their specific trigger foods⁵.
Other specialized diets exist. The specific carbohydrate diet removes all grains from the diet¹¹. It allows fresh vegetables, meat, eggs, and low-fructose fruits¹¹. The SIBO specific food guide combines the low FODMAP diet and the specific carbohydrate diet into one very restrictive plan¹¹. The bi-phasic diet uses a strict elimination phase followed by a slow reintroduction of fermentable foods¹¹.
The elemental diet is a liquid meal replacement plan⁴. The liquid formula contains proteins, simple carbohydrates, and fats that are already broken down into their simplest forms¹². The human body absorbs the liquid immediately, leaving zero food for the bacteria. Doctors prescribe the elemental diet for two to three weeks to completely starve the bacteria¹².

Selecting foods for a clear intestine

Understanding how different foods break down helps a person choose the right meals.
Proteins are safe to eat because they do not ferment into gas⁴. A person can eat chicken, turkey, lean beef, pork, fish, and eggs⁵. Firm tofu is an acceptable plant-based protein¹². The process of making firm tofu presses out the water and the fermentable sugars¹². Silken tofu keeps that liquid, so it is avoided¹². Processed meats require careful checking. Sausage and deli meats often have hidden ingredients like garlic powder, onion powder, or high-fructose corn syrup¹³. These additives deliver concentrated bacteria food straight to the small intestine.
Whole wheat, brown rice, barley, and oats have an outer bran layer¹². This layer is made of insoluble fiber. The human body cannot absorb it, so it travels slowly through the gut and feeds the bacteria¹³. To prevent a relapse, a person eats refined carbohydrates instead. White rice, potatoes, and white bread digest quickly¹¹. The enzymes in the human stomach turn these simple starches into glucose right away. Gluten-free pasta made from corn or white rice is safe⁵.
Authentic sourdough bread is an exception. Bakers make sourdough using a slow fermentation process outside the human body. Wild yeast eats the fermentable carbohydrates in the wheat flour before the bread goes into the oven⁵. Because the yeast already digested the sugars, the baked bread is usually safe to eat⁵.
Root vegetables and fruiting vegetables are the safest choices. Carrots, cucumbers, bell peppers, tomatoes, zucchini, parsnips, and eggplant have very low levels of fermentable sugars⁵. Broccoli, cauliflower, Brussels sprouts, and cabbage belong to the cruciferous vegetable family. They contain complex fibers and sugars that humans cannot digest¹². They create a lot of gas and act as fast fuel for bacteria¹².
Onions, garlic, and leeks carry the highest risk for causing a relapse. They have very high amounts of fermentable fibers¹¹. A person can use the green tops of scallions or chives for cooking because the fermentable sugars stay inside the white bulbs⁵. Most mushrooms are also avoided because they contain high amounts of the sugar alcohol mannitol¹¹.
Fruits have fructose. The human body absorbs fructose easily when the fruit also has an equal amount of glucose. If a fruit has more fructose than glucose, the extra fructose travels slowly through the gut and ferments¹³. Apples, pears, mangoes, cherries, and watermelon have high amounts of extra fructose¹². Apples and pears also contain sorbitol, giving the bacteria two different types of food at once¹³. Strawberries, blueberries, oranges, lemons, kiwi, cantaloupe, and grapes have balanced sugars and are absorbed easily⁵.
All dried fruits are avoided. Raisins, dates, prunes, and dried figs are highly concentrated sources of sugar⁵. Fruit juices flood the small intestine with sugar too quickly, so they are also restricted⁵.
Cow’s milk, yogurt, and soft cheeses like ricotta or cream cheese contain lactose⁵. If a person does not have the lactase enzyme in their small intestine, lactose ferments and causes gas and diarrhea⁴. The process of making hard cheese removes the lactose. Hard, aged cheeses like parmesan, cheddar, and Swiss are safe to eat⁵. Butter and ghee are made of fat and have almost zero milk sugars⁵. Lactose-free cow’s milk is safe because the manufacturer adds the lactase enzyme to the milk, which pre-digests the sugars⁵. Almond milk, rice milk, and oat milk are safe plant-based alternatives⁵.
Walnuts, macadamia nuts, almonds, sunflower seeds, and pumpkin seeds are well-tolerated in small portions⁵. Cashews and pistachios are strictly avoided because they have high amounts of fermentable fibers¹⁵.
Table sugar and pure maple syrup have balanced amounts of glucose and fructose. The body absorbs them quickly, making them safe to eat in small amounts¹². Honey and agave nectar have too much fructose and ferment easily⁵. Sugar alcohols like sorbitol, xylitol, and mannitol are found in sugar-free gum and diet candies¹². The human body cannot absorb them. They draw water into the intestines and feed the bacteria¹². Food thickeners like xanthan gum, guar gum, and carrageenan are also highly fermentable and slow down the movement of food through the digestive tract¹².

Food texture and cooking methods

The physical texture of food affects how fast the body digests it. Tough, raw foods force the stomach to work harder. If the stomach does not break the food down completely, large pieces enter the small intestine. This slows down the transit time and gives bacteria a place to attach and feed¹⁰.
Eating soft, well-cooked foods prevents this problem²¹. Cooking vegetables breaks down their tough outer structures. Soups, stews, and slow-roasted meats are good choices because the cooking process does some of the digestive work before the person even takes a bite²¹.

Summary of food categories

Food category	Easily absorbed foods	Slowly absorbed foods
Proteins	Chicken, beef, fish, eggs, firm tofu	Processed meats with garlic or onion powder, silken tofu
Grains	White rice, white potatoes, authentic sourdough, corn pasta	Whole wheat, brown rice, barley, rye, oats
Vegetables	Carrots, cucumbers, bell peppers, tomatoes, zucchini	Onions, garlic, broccoli, cauliflower, cabbage, mushrooms
Fruits	Strawberries, blueberries, oranges, grapes, kiwi	Apples, pears, cherries, watermelon, mangoes, dried fruits
Dairy	Hard cheeses, lactose-free milk, butter	Cow's milk, yogurt, soft cheeses
Nuts	Walnuts, macadamia nuts, almonds, sunflower seeds	Cashews, pistachios
Sweeteners	Table sugar, maple syrup	Honey, agave, sorbitol, xylitol, high-fructose corn syrup

The problem with strict diets over time

Restricting fermentable foods stops bacteria from growing in the small intestine. However, staying on a strict diet forever causes other health problems.
The large intestine needs a diverse microbiome to stay healthy. The good bacteria in the large intestine survive by eating the exact same fermentable fibers that cause problems in the small intestine¹⁴. If a person follows a strict low FODMAP or low fermentation diet for a long time, they starve the good bacteria in their colon².
These good bacteria produce short-chain fatty acids. These fatty acids give energy to the cells lining the colon and support the immune system²³. Long-term restriction weakens the gut and lowers the number of beneficial bacteria¹⁴.
To fix this, a person must test their limits. Once the small intestine is free of symptoms, the person slowly adds small amounts of excluded foods back into their meals¹¹. They might find they can eat a small bowl of oats or a piece of broccoli without getting sick. This gradual expansion keeps the large intestine healthy while keeping the small intestine clear of overgrowth⁴.
This is for informational purposes only. For medical advice or diagnosis, consult a professional.

Works Cited & Scientific References 23

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