SIBO and Sugar
The Sweet and Sour Truth about Sweeteners and Your Gut Health
If you are one of the millions of people around the world suffering from SIBO (Small Intestinal Bacterial Overgrowth), IMO (Intestinal Methanogen Overgrowth), or ISO (Intestinal Sulfide Overproduction), sugar can sometimes feel like the enemy.
As you’ve searched for answers to find out what is causing symptoms like bloating, diarrhea, constipation, and abdominal discomfort, you’ve probably come across articles and forums warning about all kinds of potentially problematic foods. But sugar and other sweeteners rank amongst the most discussed, most impactful—and possibly most misunderstood—foods of all. So, it’s worth your time to familiarize yourself with the ins and outs of sugars and sweeteners, both natural and synthetic.
In this article we’ll take a deep dive into why sugar is such a big part of the diet discussion for those who’ve been diagnosed with or suspect they may have a microbial overgrowth. We’ll talk about how sugar and other sweeteners affect your gut microbiome (the community of microorganisms living in your digestive tract), clarify some common myths, and offer some practical, science-backed strategies for choosing sweets that are easier on a sensitive gut.
What are SIBO, IMO, and ISO?
SIBO, IMO, and ISO are all forms of gut microbial imbalances. In SIBO, excess bacteria accumulate in the small intestine, producing hydrogen gas and causing symptoms like bloating, abdominal discomfort, and changes in bathroom habits. IMO involves methane-producing archaea rather than bacteria, often leading to constipation. ISO occurs when sulfide-producing microbes generate too much hydrogen sulfide gas, which is more often linked to diarrhea. Each condition involves different microorganisms and gases—hydrogen, methane, or hydrogen sulfide—but all share a common root in disrupted gut motility and microbial imbalance.
So, what does any of this have to do with sugar? We're glad you asked, because that's what the next sections are about!
How is sugar related to microbial imbalances?
In each of these cases of microbial imbalances, the microbes (bacteria and/or archaea) start to flourish in types and quantities that are abnormal for your gut’s microbiome. But, like all organisms, these microbes don’t simply exist and multiply on their own. They need fuel to live and carry out biological functions, just like we need food and water to survive and stay healthy.
Microbes involved in these imbalances flourish on fermentable carbohydrates, particularly sugars that are readily broken down for energy. Their fermentation of these sugars produces gases, such as those described above, as metabolic byproducts. So, sugars have the potential to feed the microbes living in your gut, enlarging their populations and potentially exacerbating any symptoms you have that are related to the underlying microbial imbalance.
So, does sugar cause SIBO?
It’s important to note that while sugars and other fermentable carbohydrates feed the microorganisms in your gut, they don’t directly cause the imbalance itself. The relationship between sugar and SIBO is more nuanced than that. A large body of research now suggests that microbial overgrowths are actually the consequence of disruptions in your gut’s motility and function that have caused problems with your natural, cyclical ability to move food through your gastrointestinal system.
Potential root causes of microbial overgrowths include cases of foodborne illness (“food poisoning”), IBS (Irritable Bowel Syndrome), complications from abdominal surgery, structural problems or blockages in the small intestine, Crohn’s disease, scleroderma, celiac disease, and diabetes. In his landmark publication The Microbiome Connection, renowned gastroenterologist Dr. Mark Pimentel, Executive Director of the Medically Associated Science and Technology Program at Cedars-Sinai, puts it this way: “Any factor that slows down the speed of flow [of food] through the small intestine has the potential to cause [microbial] overgrowth”.
By themselves sugars and fermentable carbohydrates do not cause SIBO, IMO, or ISO. But, they can certainly feed your overgrowth, increase gas production, and therefore worsen your symptoms. So, it is still very important to understand more about sugar as it relates to your condition. Let’s now take a look at sugar and other sweeteners, so you can see what they are and how they might be affecting you.
Natural Sugars: How They Differ and Why It Matters
We all know the word “sugar,” and when you hear it you probably conjure an image of a bowl of delicious sparkly white granules you dump in your morning coffee, or you think about your Mom warning you that too much Halloween candy will rot your teeth. But how many of us really stop to think about what sugars are?
Sugars are simple carbohydrates—organic molecules made of carbon, hydrogen, and oxygen—that the body can quickly break down into energy in your cells. Though it’s easy to think of all sugar as being the same (that familiar bowl of white crystals) there are actually many different kinds, each with slightly different structures and effects in the body.
Common Types of Natural Sugars
Natural Sugar | Type | Common Sources | Gut Impact |
|---|---|---|---|
Glucose | Monosaccharide (single sugar) | Fruits, vegetables, honey, grains | Main energy source for the body; absorbed directly into the bloodstream |
Fructose | Monosaccharide (single sugar) | Fruits, honey, some root vegetables | Naturally sweet; metabolized by the liver |
Sucrose | Disaccharide (glucose + fructose) | Table sugar, fruits, some vegetables | The most familiar “sugar” in everyday diets |
Lactose | Disaccharide (glucose + galactose) | Milk, yogurt, other dairy products | Can cause symptoms in people with lactose intolerance |
Galactose | Monosaccharide (single sugar) | Dairy (as part of lactose) | Combines with glucose to form lactose |
Maltose | Disaccharide (glucose + glucose) | Sprouted grains, malted foods | Formed when starch breaks down during digestion or fermentation |
Which natural sugars are better for people with SIBO, IMO, and ISO?
This is a complicated question, because naturally occurring sugars aren’t inherently “bad” or “good” across the board. Like most medical topics, the answer is nuanced and depends largely on an individual’s personal physiology and medical history, so it is highly recommended that you discuss your overall health and nutritional choices with your healthcare providers.
As a general rule, the faster and more efficiently a specific type of sugar is absorbed in your system, the less likely it is to significantly contribute to your microbial overgrowth and related symptoms. This is due to the mechanism we described earlier: when fermentable carbohydrates linger longer and/or travel further in your system than normal without being swept out by your intestines’ natural cleaning cycle, they are more available to be used as fuel by the microbes affecting your microbiome.
For many people with SIBO, glucose and sucrose are generally the most tolerable sugars because they are absorbed efficiently in the small intestine, leaving little behind to ferment. By contrast, fructose and lactose are more likely to trigger symptoms such as bloating, gas, or diarrhea, especially if your digestive system already struggles with malabsorption or intolerance of these sugars.
In IMO, methane-producing archaea thrive on fermentable sugars like fructose and lactose. Reducing these sugars may help decrease gas production and support better gut motility.
For those with ISO, the concern isn’t as much with the sugar itself, but how certain carbohydrates can indirectly influence sulfur metabolism in the gut. Sulfide-producing bacteria rely on sulfur compounds from protein and dietary sources, but they also depend on hydrogen gas, a byproduct of carbohydrate fermentation. Diets high in poorly absorbed carbohydrates can increase hydrogen availability, giving these microbes more to feed on.
For detailed information about which foods (especially sugar-containing foods) to eat or avoid, or for a comprehensive look at special diets for patients with SIBO, IMO, ISO and IBS symptoms, please see our detailed article called “Eating with SIBO”.
Sugar Alcohols: Why They Can Worsen SIBO Symptoms
One of the most confusing aspects of the sugar discussion is a group of compounds called sugar alcohols or polyols. (They are easy to spot as most of them end in “-ol”.) Sugar alcohols are compounds that can be found in nature in small amounts, most commonly in fruits and vegetables. But they are now usually industrially manufactured in large quantities for our commercial food supply. So most sugar alcohols we consume are more synthetic than natural. They start from sugars derived from crops like corn or beets, but are generally modified to make them lower in calories and less sweet.
Despite the name, they are not actually sugars or alcohols in the usual sense. They’re a hybrid molecule that the body only partially digests and absorbs, so they typically reduce the calorie intake you might have from eating a similar food with typical, absorbable sugars. Because of this, they are often used as sugar substitutes and marketed in “sugar-free”, “low-carb”, or “diet” foods.
Common Types of Sugar Alcohols
Sugar Alcohol | Common Sources & Uses | Gut Impact |
|---|---|---|
Sorbitol | “Sugar-free” gums, candies, some fruits (apples, pears, prunes) | Poorly absorbed, easily fermented, often causes bloating and diarrhea |
Mannitol | Cough syrups, “low-carb” foods, mushrooms | Poorly absorbed, can worsen gas and loose stools in sensitive people |
Xylitol | Toothpaste, mints, gum, “diabetic” sweets | Moderately absorbed, may cause GI upset, but generally less fermentable than sorbitol & mannitol |
Erythritol | Keto snacks, protein bars, some beverages | Mostly absorbed in the small intestine, but can still cause discomfort in large amounts |
Isomalt / Maltitol | Baked goods, chocolates, protein bars | Partially absorbed, can cause bloating and flatulence when overconsumed |
As you can see from the table, sugar alcohols can be sneaky–they are often used as ingredients in processed snacks and even some non-food items like toothpaste and gum. And unless you are checking all of your ingredients, they can be easy to miss.
While sugar alcohols aren’t inherently “bad” for all people, they are usually higher up on the list of food ingredients to avoid if you have SIBO, IMO or ISO. Since they are designed to not be fully or easily absorbed, they stick around in your intestines and travel farther in your digestive tract, where they can feed all those multiplying populations of microbes. For this reason it is usually recommended that most patients limit or avoid them.
Artificial Sweeteners: Why Sugar-Free Doesn't Mean Symptom-Free
One of the most asked questions for people with microbial overgrowths, IBS, or IBS-like symptoms is how to handle all of the artificial sweeteners available in today’s food. With so many different kinds of sweeteners in our modern food supply (all with different brand names and marketing strategies) it can be a very difficult task to keep them all straight!
While most artificial sweeteners are technically non-fermentable, their impact on gut health may still be significant or problematic. In many people with SIBO, IMO, or ISO, the main concern isn’t necessarily gas production, but rather how certain sweeteners may influence gut motility and decrease the richness and diversity of the gut microbiome.
Common Types of Artificial Sweeteners
Artificial Sweetener | Brand Name & Common Uses | Gut Impact |
|---|---|---|
Aspartame | Equal, NutraSweet, found in diet sodas, sugar-free desserts | Generally not fermentable, may affect gut signalling and motility less than other choices |
Sucralose | Splenda, diet drinks, baked goods, protein powders | Poorly absorbed, mostly excreted unchanged, but may alter gut microbiota or reduce beneficial bacteria |
Saccharin | Sweet’N Low, tabletop sweetener, packaged foods | Non-fermentable, may contribute to microbiome disruption or glucose intolerance |
Acesulfame Potassium (Ace-K) | Sunett, Sweet One, often blended with sucralose or aspartame | Not metabolized by body or microbes, some studies show impact on microbial balance |
Neotame | Some sugar-free baked goods and beverages | Similar to aspartame, minimal fermentation, but very little data available about gut impact |
Advantame | Some processed foods and beverages | Similar to aspartame, minimal fermentation, but very little data available about gut impact |
A recent controlled study from Cedars-Sinai studied the impact of various non-sugar sweeteners on a population of enrolled subjects. Compared to controls in the study (those not taking any non-sugar sweeteners) scientists noted significant differences in both stool and duodenal (small intestine) microbiomes of those subjects consuming the artificial sweeteners.
Highly respected endocrinologist, professor, and lead author of the study, Dr. Ruchi Mathur, MD, summarized some of its findings:
“Artificial sweeteners are not benign for the microbiome of the gut. We found that the richness of the bacteria in the small bowel was less in those subjects consuming non-aspartame non-sugar sweeteners when compared to controls, whereas bacterial richness in those consuming aspartame was similar to controls…”
In short, while artificial sweeteners may limit some of the concerns related to fermentation that are seen with some sugars and most sugar alcohols, evidence suggests that they may still contribute to microbiome disruption, erratic motility, and uncomfortable symptoms associated with microbial overgrowths. Of the most common artificial sweeteners on the market, aspartame has shown less impact on microbiome diversity than the others. But other potential health concerns regarding aspartame still make it difficult for some practitioners to confidently recommend. For this reason, it is generally advised to limit or avoid these ingredients whenever possible.
Naturally Derived Sweeteners: When “Natural” Doesn’t Always Mean Gut-Friendly
Naturally derived sweeteners like stevia, monk fruit, and allulose are often promoted as healthier, “gut-friendly” options, but even these should be approached with care if you’re managing SIBO, IMO, or ISO. While they come from natural sources and don’t typically feed gut microbes in the same way sugars or sugar alcohols do, Dr. Mark Pimentel and the Cedars-Sinai team caution that some of these sweeteners can still affect motility or disrupt the gut’s microbial rhythm.
In particular, Dr. Pimentel has noted that emerging data may suggest that stevia could interfere with the migrating motor complex–the natural wave-like motion that clears bacteria from the small intestine between meals. This makes even natural sweeteners potentially problematic for those already struggling with motility-related overgrowth.
Monk fruit and allulose may be more promising alternatives in the long run, because they are generally considered Low FODMAP and more tolerated in small amounts. But the Low Fermentation Eating (LFE) plan–which is often considered the gold standard for eating while managing SIBO–still lists them under “Foods to Avoid”. This cautious stance reflects the current lack of specific research, which makes it difficult to conclusively predict how individuals with microbial overgrowths will respond.
In short, naturally derived sweeteners may be better tolerated than artificial ones or sugar alcohols, but they’re not a free pass. Many physicians recommend you use them sparingly, pay attention to your body’s response, and focus on overall meal balance rather than chasing the perfect substitute for sugar.
Don’t give up! You deserve answers.
Finding balance with sugar and sweeteners can feel overwhelming when you’re managing SIBO, IMO, or ISO—but it doesn’t have to be. The goal isn’t to eliminate sweetness from your life, but to understand how different sugars and substitutes interact with your unique gut environment. By focusing on motility, choosing well-absorbed carbohydrates, and paying attention to your body’s responses, you can make informed decisions that reduce symptoms without feeling deprived. Partnering with your healthcare provider and using evidence-based tools—like the Trio-Smart 3-Gas Breath Test—can help you better understand your gut’s activity and create a plan that supports both comfort and long-term gut health.
FAQ
Does sugar cause SIBO?
No. SIBO develops when motility or gut function is impaired, allowing bacteria to accumulate in types and numbers that adversely affect your microbiome. Sugar doesn’t cause the imbalance, but it can feed it once present.
Does cutting out sugar cure SIBO?
Not by itself. Reducing fermentable sugars can ease symptoms, but resolving SIBO requires identifying and treating the underlying cause—often with medical testing and targeted therapies like antibiotics and diet change. For more information on this, please see our article on Treatment Plans for SIBO, IMO, and ISO.
Which natural sugars are safest?
Glucose and sucrose are generally best tolerated. Fructose and lactose often cause more bloating and discomfort in people with SIBO or malabsorption.
Are artificial sweeteners safe for SIBO?
They’re not fermentable, but studies show some can disrupt gut bacteria or slow motility. Limiting or avoiding them is usually recommended.
Are sugar alcohols okay to eat?
Usually not. Because they aren’t fully absorbed, they linger in the gut and often worsen gas and bloating in SIBO, IMO, and ISO.
Can SIBO affect blood sugar or cravings?
Yes. Microbial imbalances can interfere with digestion and nutrient absorption, sometimes contributing to sugar cravings or fluctuating blood sugar levels.
What’s the best way to manage sugar with SIBO?
Choose simple, well-absorbed sugars when needed, avoid excessive “sugar-free” or high-fiber additives, and follow a Low-Fermentation Eating plan to support healthy motility and balance.
References:
https://pmc.ncbi.nlm.nih.gov/articles/PMC3099351/
Pimentel, M., & Rezaie, A. (2022). The Microbiome Connection: Your Guide to IBS, SIBO, and Low-Fermentation Eating. Harper Wave, p. 78
https://sibosense.blog/2018/04/28/sibo-chat-dr-pimentel-food-diet/