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Is Sugar Toxic to Your Gut?

Updated: May 30

Do sugar and sweeteners really harm the gut?

By Austin Perlmutter, MD



  • Gut health is emerging as a central driver of overall health

  • Gut health is a reflection of things like the state of our gut cells, gut immune system, "leakiness" of the gut lining and the makeup of the bacteria in our gut microbiome

  • Diet is thought to be one of the biggest variables that alters gut health, including the health of the microbiome

  • Some primarily pre-clinical data connects excess added sugar consumption with worse gut health, but it's relatively limited

  • Other primarily pre-clinical data suggests that sugar alternatives including sugar alcohols and artificial sweeteners may correlate with worse gut health

  • Some ways in which gut health may be damaged by sugar and alternative sweeteners include increased inflammation, a leakier gut and a less healthy gut microbiome

  • On the whole, avoiding excess added sugar and limiting sugar alternatives may make sense for overall wellness, including gut wellness. However, human data at this time is limited when it comes to the link between sugar and sweetener consumption and worse gut health outcomes.

Across the field of nutrition there are active debates over just about everything. Should we eat more fish? Are beans packed with toxic lectins? Are eggs healthy or cholesterol-packed fat bombs? Yet there’s one recommendation that most experts seem to agree on: we all benefit from eating less added sugar. One potential reason relates to the gut, especially with research showing that gut health may represent a central pathway to multiple disease and health states. So how do gut health and sugar consumption connect? And what about artificial and alternative sweeteners? Here’s the science you need to know.

What does the research say about dietary sugar and gut health?

Remember that your gut microbiome is the community of tens of trillions of microbes, that live, work and die in your GI tract (especially your large intestine). The health and composition of the bacteria in your gut microbiome has been the subject of recent intense research as it relates to human wellness. One of the most important insights about our gut microbiome is that it is dynamic, and changes in response to our diet.

It's been established that eating too much added sugar in our diets is a risk factor for weight gain, metabolic diseases like diabetes and potential even brain issues like Alzheimer’s disease. One way may be through the gut microbiome. In primarily animal models, research shows that consumption of a diet high in added natural sugars led to unhealthy changes in the gut microbiome (called dysbiosis), as well as increased gut inflammation and a leakier gut lining. Recent human studies have also indicated that a high sugar diet may create dysbiosis in the mouth, long before the sugar reaches our lower GI tract.

What about sugar substitutes?

If excess consumption of natural sweeteners poses a risk to gut health, should we instead turn to artificial and other low-calorie alternative sugar alternatives? In the last decades, a number of these sugar-substitutes have been marketed as safer or healthier alternatives to natural sugars. They range from artificial sweeteners like aspartame and sucralose to sugar alcohols like xylitol and erythritol to naturally sweet molecules like stevia and monkfruit. We’re now learning that despite the initial excitement, consuming some of these “sugar-free” options is linked to worse metabolic health, including weight gain. But are they better for the gut?

Here again, most research is pre-clinical. Yet there are indications from this work that these sugar alternatives may not be as great for the gut as once hoped. Some data have suggested that sugar substitutes may alter the health of the gut lining, while other studies indicate a potential to increase dysbiosis. Emerging human data suggests the potential for differential effects of various sweeteners on markers of gut health.

What’s the take-home message?

Protecting gut wellness is and will continue to be a major talking point when considering a wide variety of health outcomes. At this time, most of the evidence that eating too much sugar and sugar substitutes could damage gut health comes from test tube and animal research rather than human trials. Conversely, there’s better human data to suggest that consumption of a minimally processed diet rich in whole foods is associated with a healthier gut. As is generally the case, it’s tough to isolate human nutrient consumption in isolation. People consuming diets rich in added sugars and sugar alternatives are often those engaging in a less healthy lifestyle and an overall lower quality diet.

In the coming years, we’re sure to get far more information on the relative role of sugar and sugar substitutes in multiple aspects of our health, including gut health. In the interim, it’s unlikely that overconsumption of either of these food groups is doing us or our GI tracts any favors. Choosing a diet lower in added sugars and sweeteners and high in a diversity of whole foods including colorful fruits, vegetables, nuts and seeds and minimizing exposure to ultra-processed foods and beverages may make the most sense to most people seeking dietary steps for gut health, though personalization with a healthcare practitioner is always optimal.

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