Your GLP-1 Might Be Affecting Your Gut More Than You Think

The link between slowed gut motility and bacterial overgrowth

GLP-1 medications (such as Ozempic®, Wegovy®, Mounjaro®, and Zepbound®) have become one of the most widely discussed topics in health and wellness over the past several years. Television commercials highlight their potential benefits, news coverage scrutinizes their risks, and public conversation is increasingly filled with speculation about who is taking them and how different options compare.

GLP-1 based medicines (including newer combination therapies that activate GLP-1 plus other gut hormone receptors) are used for type 2 diabetes, heart disease, and weight management. Recent polling indicates that about 12% of American adults (approximately 30 million people!) are currently taking these drugs for one of these conditions.

With usage being so prevalent, this raises a very important question: what do these medications do to your gut, and could they increase your risk of developing microbial imbalances like SIBO, IMO, or ISO? This is especially important for those people who have been diagnosed with IBS or IBS-like symptoms, including bloating, diarrhea, constipation, and abdominal pain. These conditions can greatly affect your health and quality of life, so it’s understandable to ask whether anything might worsen these symptoms or increase the risk of further complications.

This article takes a practical, science-grounded look at what’s known and what’s still emerging, with a special focus on the gut mechanisms most relevant to SIBO (Small Intestinal Bacterial Overgrowth), IMO (Intestinal Methanogen Overgrowth), and ISO (Intestinal Sulfide Overproduction).

What do we mean by “GLP-1 medications”?

When people talk about GLP-1 medications, they are referring to drugs that mimic the effects of glucagon-like peptide-1 (GLP-1), a hormone the body naturally releases after eating. GLP-1 plays a key role in digestion and metabolism by helping regulate blood sugar, slowing how quickly food leaves the stomach, and sending signals to the brain that promote feelings of fullness. Medications in this class are designed to amplify or prolong these natural signals.

These therapies are often recognized by brand names, but rather than focusing on any specific product, this article discusses them as a class of drugs. While each medication has its own molecular structure and mechanism of action, as a class they all share certain effects on the digestive system, especially on motility, which we’ll discuss next.

The gut effect that matters most: slower motility

Gut motility refers to the coordinated muscular contractions that move food and liquids through the gastrointestinal tract, helping regulate digestion, nutrient absorption, and cleansing of your digestive system. When your gut is functioning at its best, your motility is regular and routine, which allows the microbes that are always present, such as bacteria and archaea, to exist in balanced, healthy quantities.

One of the most consistent findings in humans is that GLP-1 signaling slows gastrointestinal motility. That includes slowing stomach emptying and, in many cases, slowing aspects of small intestinal movement, as well. GLP-1 medications do this by design, as slower transit helps curb blood sugar spikes and contributes to appetite reduction, so this is generally considered advantageous for treatment of type 2 diabetes and weight management.

However, this slower transit can be detrimental to your gut health and your microbiome (the community of microorganisms that live in and aid your digestive tract.) Decades of research have shown a significant link between slowed motility and harmful microbial overgrowths.

Dr. Mark Pimentel, MD, Executive Director of the Medically Associated Science and Technology Program at Cedars-Sinai, and a leading expert on microbial overgrowths, puts it this way: “Any factor that slows down the speed of flow [of food] through the small intestine has the potential to cause [bacterial] overgrowth.”

This is important for patients assessing their SIBO risk, because studies suggest GLP-1 signaling can inhibit aspects of the Migrating Motor Complex (MMC). The MMC is often described as the gut’s “cleaning wave” since it’s a repeating pattern of contractions that occurs between meals, helping move residual food and microbes downstream through the small intestine. When the MMC is slowed or suppressed, motility is reduced, making it easier for microbes to accumulate in the small intestine.

A large retrospective database analysis conducted in 2025 specifically examined whether GLP-1 therapies may be associated with increased short-term risk of a SIBO diagnosis, compared to other diabetes treatments. The analysis found that people taking GLP-1 or GLP-1/GIP drugs were diagnosed with SIBO about twice as often as those taking other diabetes medications.

However, it is important to note that this study was observational in nature, not a randomized clinical trial designed to establish cause and effect. As a result, additional prospective and controlled studies are needed before definitive conclusions can be drawn.

Does slower motility automatically mean you'll get SIBO?

While slower gut motility is a well-established risk factor for bacterial overgrowth, it does not guarantee that you will develop SIBO, IMO, or related conditions. There are many other variables that can contribute to a patient’s risk of developing a microbial overgrowth, including:

Low stomach acid (hypochlorhydria) – Reduces the stomach’s ability to limit bacterial entry into the small intestine
Impaired digestive secretions – Decreased bile acids or pancreatic enzymes can allow microbes to grow unchecked
Structural changes to the gut – Anatomical alterations or surgical changes can trap bacteria and promote overgrowth
Disrupted gut immune defenses – Weakened immune regulation can impair normal microbial control
Previous gastrointestinal infections – Infections such as foodborne illness can cause lasting changes that increase susceptibility to overgrowth
Frequent or repeated antibiotic use – Antibiotics can disrupt microbial balance and enable opportunistic overgrowth
Dietary patterns that promote fermentation – Excess fermentable carbohydrates can fuel microbial proliferation
Underlying metabolic or systemic conditions – Certain chronic conditions can indirectly affect gut regulation and balance
Altered gut–brain signaling – Disruptions in neural communication can affect digestion and microbial balance

Development of microbial overgrowths and their associated symptoms is often the result of multiple risk factors aligning to amplify imbalances in your gut microbiome.

For example, Post-Infectious IBS (PI-IBS)—IBS that develops after a bout of foodborne illness—represents an illness pathway of growing clinical interest. Each year, millions of Americans experience food poisoning, and research suggests that approximately 10–11 percent or more may go on to develop prolonged IBS or IBS-like symptoms. In this context, a patient who had food poisoning months earlier may already be at increased risk for microbial overgrowth, and additional slowing of gut motility (such as that associated with GLP-1 therapy) could further compound that risk.

Do GLP-1 medications make the microbiome “less healthy”?

There is no single definition of a “healthy” microbiome. But what is well-supported by science is that diet is a major driver of microbiome composition and diversity. What you eat, how much you eat, and when you eat it matters a great deal to your gut. GLP-1 usage often changes your eating patterns, resulting in lower food intake, smaller meals, and less food variety. If appetite suppression leads to a highly restrictive or repetitive diet, microbiome diversity may decline over time.

However, it doesn’t have to be this way. Some people may actually improve the quality of their diet while on GLP-1 by focusing on high-quality food intake and more regular eating patterns. By choosing healthier, low-fermentation foods, limiting alcohol consumption and snacking, and creating more structure to your meal times (the exact types of directives you are likely to receive to aid in diabetes control and weight management) you can actually produce more favorable shifts in your microbiome.

Putting it all together

GLP-1 medications provide clear benefits for many people, particularly in the treatment of type 2 diabetes, cardiometabolic disease, and obesity. At the same time, their well-documented effects on gut motility raise reasonable questions about digestive health, especially for individuals with IBS, a history of food poisoning, constipation, or other risk factors for microbial overgrowth.

Current evidence doesn’t point to a specific causal relationship that directly links GLP-1 drugs and microbial overgrowths, but the underlying mechanics and possible resulting effects certainly warrant a degree of caution. Slower gut motility can increase susceptibility to conditions like SIBO, IMO, or ISO in some people, while others may tolerate GLP-1 therapy with minimal gastrointestinal impact. In many cases, the benefits of improved blood sugar control or meaningful weight loss may still outweigh potential gut-related risks, even when those risks deserve some consideration.

As always, the most constructive approach is informed, personalized decision-making in conjunction with your healthcare provider(s). Being aware of symptoms and understanding individual risk factors can help guide your next steps. For some patients, objective testing may be a useful part of that process. Breath tests like the Trio-Smart 3-Gas Breath Test can offer important insights into whether you have an overgrowth, and what kind of overgrowth it is.

Ultimately, GLP-1 medications are neither universally harmful nor universally benign to the gut. With the right information and appropriate monitoring, many people can benefit from these therapies while minimizing unintended digestive effects.

Frequently Asked Questions

Can GLP-1 medications cause SIBO, IMO, or ISO?

There is no definitive evidence that GLP-1 medications directly cause microbial overgrowths. However, because they slow gut motility, they may increase susceptibility in some individuals—particularly those with existing risk factors such as IBS, constipation, or prior gastrointestinal infections.

Does everyone who takes a GLP-1 experience slowed gut motility?

Most people experience some degree of slowed gastric emptying, but the extent and clinical impact vary widely. Some individuals tolerate these changes without significant digestive symptoms, while others may notice bloating, constipation, or discomfort.

If I’m on a GLP-1, does that mean I will develop SIBO?

No. Slower motility is a risk factor, not a guarantee. Microbial overgrowths typically develop when multiple factors align, such as impaired digestion, immune changes, prior infections, or dietary patterns.

Are people with IBS at higher risk when taking GLP-1 medications?

People with IBS, especially those with constipation-predominant symptoms or a history of post-infectious IBS, may already have altered gut motility, which could increase vulnerability. This does not necessarily mean GLP-1 therapy is inappropriate, but it does often mean symptoms should be monitored more closely.

Can GLP-1 medications affect the gut microbiome?

At this time there is no conclusive evidence that GLP-1 medications directly “damage” the microbiome, but changes in appetite, meal size, and food variety can influence microbial diversity over time. Diet quality and regular eating patterns play a major role in determining microbiome health.

Is breath testing useful for people experiencing GI symptoms on GLP-1 therapy?

For patients with persistent or unexplained digestive symptoms, breath testing can be a helpful diagnostic tool. Tests such as the Trio-Smart 3-Gas Breath Test can help identify whether SIBO, IMO, or ISO is present, supporting more informed clinical decisions.

Should gut-related risks outweigh the benefits of GLP-1 therapy?

Not necessarily. For many individuals, the benefits of improved blood sugar control, cardiovascular risk reduction, or meaningful weight loss may outweigh potential gut-related risks. The goal is not avoidance, but informed use: balancing benefits, symptoms, and individual risk factors with guidance from a healthcare provider.

What happens when I stop taking a GLP-1 medication?

After stopping a GLP-1 medication, its effects on gut motility gradually diminish as the drug leaves the system. For some individuals, intestinal movement returns closer to baseline, which may reduce symptoms related to slowed transit, such as bloating or constipation. However, any underlying risk factors for microbial overgrowth, such as IBS or prior gut infections, may still be present and can continue to influence SIBO, IMO, or related symptoms.