Understanding Small Intestine Bacterial Overgrowth

In the past 10 years, there has been increasing evidence that small intestinal bacterial overgrowth (SIBO) plays a role in the cause of irritable bowel syndrome. Patients have consistently asked for even more details on diet for SIBO. This new diet instruction helps provide that added detail. However, in order to understand why a diet can be helpful, you must understand what small intestinal bacterial overgrowth (SIBO) is, and why it happens.


How the intestine works

The intestines are compartmentalized into the esophagus (food pipe), stomach, small intestine (where all the food is digested) and colon (large intestine) (where only waste is handled and dehydrated). The slower the gut moves, the easier it is for bacteria to stay in any place. When you eat, food quickly travels through the esophagus and into the stomach. The stomach acid helps denature proteins and also kills bacteria on the food you eat. The food is then delivered very slowly from the stomach into the small intestine to be further digested and absorbed into your blood. However, not all food can be processed by humans. Humans cannot process certain carbohydrates such as cellulose (most plant matter contains this). The whole time from eating to completing digestion takes about 2 hours. The small intestine is about 3.5 meters long.


Although the colon or large intestine functions to absorb water, almost 90% of the water was absorbed by the small intestine already. So, the colon really is just for the finishing touches in dehydrating the stool, making the stool solid, and the time of passing it more convenient.


Eating and Fasting

It is very important for you to understand these two concepts before implementing the diet. The human intestine is made of nerves and muscles that help move spread and absorb food. However, there are two “modes” for the intestine. These are “eating mode” and “cleaning mode”.


When you are eating, the bowel is bathed in all the food you eat and the bowel is busy mixing, spreading and absorbing the food. When you are not eating, the bowel needs to clean up. This is most important in the small intestine where food is absorbed. In the small intestine, every 90 minutes, there is a strong, repetitive and moving wave that is called the “housekeeper wave”. It is responsible for cleaning the small bowel pushing all the leftover non-digestible material into the colon so that the next time you eat your small bowel will be clean and ready.

What is small intestinal bacterial overgrowth (SIBO)?

The human bowel has more bacterial cells than even the number of human cells in our body. This is incredible and also normal. Almost all of these bacteria are in the colon or large intestine. The reason for this is that the colon is the slowest area. The slower the bowel, the easier it is for bacteria to grow and establish. On the other hand, the small intestine normally has a low number of bacteria. This is because of stomach acid, pancreas and bile juices, the faster movement of the small bowel but most importantly the cleaning waves mentioned above.

Bacteria overgrowth (SIBO) is not an infection. It is not “bad” bacteria. It is simply the situation of having too many bacteria of the normal kind in the small intestine. They don’t belong there in high numbers.

Why does SIBO occur?

This is complicated and changes with more research. At the moment there are many reasons for SIBO. Anything that reduces gut flow will cause SIBO. This could be blockages in the bowel, narcotic use, and other causes of mechanical slowing. However, most recently, there is link between irritable bowel syndrome (IBS) and SIBO and this is now the most common reason for SIBO. In the case of IBS, it is believed that food poisoning (getting really sick from special pathogenic bacteria after eating bad food like Salmonella, E. coli, Campylobacter, Shigella and even C. Difficile) in the past leads to this. At Cedars-Sinai Medical Center, we have determined that food poisoning and a toxin they all have, causes nerve damage to the small intestine. In part, this causes a reduction in the number of cleaning waves of the small intestine and this leads to bacterial overgrowth.



Think about what we said above the colon is almost a meter long and only gets leftover waste. The small bowel is around 3.65 meters long and is bathed in fresh, easy to use, new food. In a normal human when trash gets to the colon this is the leftover stuff that we could not digest. We could not digest it because it is hard to digest. The bacteria also have a hard time digesting it but can digest it slowly. This produces a little gas as is normal for everyone. The colon is only around a meter long so if there is gas in there, it doesn’t fill much space. Now think of the small bowel and bacterial overgrowth. You have 3.65 meters of bowel, now with too much bacteria in it, bathed with easy to digest fresh food. Wind/gas is easy to produce for bacteria from this material and the small bowel takes up a lot of space. This means a lot of bloating, and with that comes pain and discomfort.


How to Eat

Now that you understand how things are supposed to work in the gut, you can start to understand how diet can help SIBO and more importantly keep it away. Unfortunately, diet alone is never enough to treat SIBO. We use the diet as a way of reducing recurrences.

Every time you put food in your mouth, the computer program of the gut switches from cleaning mode to eating or digesting mode. If you put food in your mouth every hour of the daytime, you will never have cleaning waves. So the first recommendation is to eat the same amount as you normally do but that you eat it as distinct mealtimes.

  • Eat breakfast then don’t eat anything till lunch and the same between lunch and dinner. Even if you have a reduced number of cleaning waves, there may be some that come through if you spend enough time not eating between meals.

  • Allow at least 4-5 hours between meals.


2. Don’t eat right before bed. Nighttime is the longest time you are not eating. This is the time of the day where the greatest number of cleaning waves are seen.


3. Don’t snack all the time. More snacking, less cleaning waves, more fermentation and bloating.


Before we get to specifics, there are concepts you need to understand. The type of food is very important. An example is this: Oil can be left on the counter or in your cupboard, it does not need to be refrigerated because ordinary bacteria cannot digest fats in isolation. So the oil does not spoil. However, if you put a tablespoon of sugar in that oil, it will spoil, because bacteria like sugar. But keep reading because it is not that simple since humans like and need sugar too.


Not everything you eat is used by your body, that’s why you have stool. Your body takes what it knows how to get calories from and the rest goes out as waste. Whatever you cannot digest feeds the bacteria in the gut, and when carbohdyrates and sugars are fermented, air is produces (methane).


Sugars are an important topic. Humans need sugar and bacteria use sugar. Some sugars are easier to digest than others for humans. Table sugar is easily used by humans so we utislise it before bacteria in the lower gut can. There are other sugars that humans don’t absorb easily, and these will travel further down the gut and be utilised by the bacteria in the gut. The table summarizes these


Chewing g and plant gums are a big problem. Gum often contains alcohol sugars like sorbitol. The “ol” at the end of the word usually means it is an alcohol sugar. Many of these sugars are synthetically designed not to be absorbed by humans. No sugar for you but all of it for the bacteria.

When bacteria get sugar, they are most active in producing gas and therefore symptoms.


Another principle with sugars is the concept of carbohydrates. Carbohydrates are long chains of sugars. Some types of sugars humans can use, some they cannot. Most plant carbohydrates are cellulose based and not digestible by humans. However, bacteria can digest these.



Now that you understand these concepts, these are the specifics of the diet.

Try to be normal

This diet is not designed to ruin your social life. Remember our goal is to make you a normal person both free from symptoms and your able to be with friends and family. I know for a fact that I could walk into almost any restaurant in this country and order something that would work with this diet. Go out. Eat out. Be as normal as you can. Just know what to order.


Meal structure

Eat smaller meals. Limit snacking and avoid eating 1-2 hours before bedtime. Give whatever cleaning waves you have a chance to work.


Simple Sugars

1. Avoid non-digestible carbohydrates. This includes columns 2 and 3 above. However, regular sugar is no problem. So you can eat cake, cookies, etc., made with this.

2. Dairy is a good source of carbohydrate and protein. Try to use lactaid milk. The lactose is broken down for you already.

3. Avoid yogurt. Yogurt contains some lactose and also bacteria. You have a hard time clearing the bowel so these bacteria (which also produce wind) could cause more trouble.

4. Avoid chewing gum or anything with alcohol sugars.

5. Avoid non-absorbable sugars like splenda.Stevia is fine.

6. Avoid dairy products like non-lactose-free milk, non-aged cheese and yogurt. These all have lactose in them.

7. Don’t drive yourself crazy looking at labels.



1. Simple easy to digest carbohydrates are best, such as rice, potatoes and sweet potatoes.

3. Bread should be gluten free. Avoid wheat, wholemeal and multigrain breads.

4. Nuts are fine.

5. Dark Chocolate is allowed but not milk chocolate.

6. For breakfast cereal, rice based cereals are better, but eggs or a protein-based breaky is ideal.

7. Use Gluten free pasta.

8. Avoid gluten based baked goods. Gluten free flour products are better, just watch for the sugar type.



Gluten is a protein in certain grains like wheat. Most things containing gluten are carbohydrates. A gluten free diet is usually easier to digest. Many humans don’t digest gluten well, so until your digestive system is restored, it is best to avoid gluten based foods. This means anything containing or made from: wheat, rye, cous cous, bourghal, bakers flour, spelt, kamut, etc.



Fiber is made up of indigestible long chains of sugar.

1. Do not go out of you way to eat fiber as in whole wheat bread or supplements such as Metamucil.

2. Many products now have “added fiber”. Cheerios, for example, have added fiber now to make it “healthier”. Watch for this.


1. All proteins are good and work with this diet.

2. Meats including fish, chicken, pork and beef are all ok. Be careful with restaurants, many infuse the meat with butter before cooking. Butter contains lactose. Ghee is fine.

3. Eggs are great.

4. Protein powders need to be checked. Finding one that suits you is particularly important for vegans and those who are mostly vegetarian.


1. Fatty items are allowed on this diet as long as they comply with above.

2. Just remember that a high fat diet leads to other issues if combined with high carbohydrate foods.



1. Drink plenty of water. You should have 5-8 cups of a day, between meals.

2. Avoid soft drinks. While most diet drinks have NutraSweet or aspartame (which is toxic to the body), some have changed to sucralose or splenda. This is one place you want to check the label.

3. Avoid juice.



This is probably the section we get the most questions about.

1. Avoid beans and legumes. Beans contain a special sugar-like substance humans cannot digest. Bacteria can easily digest it which creates gas.

2. Avoid cabbage, Brussels sprouts, broccoli, cauliflower and leafy vegetables. If you have a salad, make it a side salad not a salad meal.

3. No hommus. Hommus is chick pea puree. This is the worst food for SIBO.

4. You can eat anything that grows under the ground including onions, garlic, potatoes, yams, beets, carrots, turnips, etc.

5. You can eat anything that grows off a plant like capsicum, tomatoes, cucumber, zucchini, pumpkin, eggplant, peas (not the pod), etc. These are fruit vegetables.

6. Mushrooms are fine, if they suit you, shiitake is the best one to add to your cooking. Powder dried shiitake mushrooms and add them to cooking to boost the nutritional content and immune boosting qualities of the food.

7. If you want a salad, the best is a tomato, cucumber and onion salad with dressing.


1. Apples, pears and bananas are constipating and slow the gut. You can eat these but at a minimum.

2. All other fruits are fine.



Probiotics are very complicated, and is a 7 page explanation by itself. However, the simple message is all bacteria ferment. All bacteria produce gas and you have a hard time clearing bacteria from your small bowel. The same is true for the bacteria in probiotic products. We have occasional patient who say that they are better on probiotics but for the most part people with SIBO either get worse or stay the same.



Go ahead and cheat….on rare occasion. We don’t want to make you miserable. Here are some special cheats:

1. Lactose free ice cream (watch for sucralose though)

2. Hard cheeses have much lower lactose as it is used up as they are aged.

3. Cheap cakes have icing made from edible oil not dairy. Not so good for you but tastes great and sometimes you just want to be bad.


 (Ref: Dr Sierbeker - edited MW )

Monica Williams 

0409 188 173

  • Facebook - White Circle
  • Google+ - White Circle
  • LinkedIn - White Circle


Emerald & Malvern, Victoria

+ Phone / Skype Sessions

Please no hawking, cold-canvassing or sales calls, thanks.

DISCLAIMER : We do not diagnose nor treat 'disease', rather we offer education and a personal relationship in support of people as they move through their own life journey. The body self-heals when supported with the optimal conditions. No-one else can heal us, only we can. We seek to support our clients in this process of self-alignment.; identifying obstacles to  the body's innate self healing process, while supporting it with what is needed. We make no claims, medical or otherwise, and we are not a substitute for medical care. 

© 2019 Healthier By Choice. 

The information on this website is for general education only.