Bloating and bowel changes on weight loss drugs? It could be SIBO

If you’ve started taking a weight loss injection like Wegovy or Mounjaro and your digestion has taken a turn for the worse, you’re not imagining it.

These types of medication can be helpful for managing weight and blood sugar, but they may also cause excessive gas, cramps, nausea, and erratic bowel movements.

One of the consequences is the potential to trigger or worsen SIBO (small intestinal bacterial overgrowth).

Here’s how that happens, and what you can do about it.

What do weight loss injections do?

Wegovy (semaglutide) and Mounjaro (tirzepatide) are part of a class of medications known as GLP-1 receptor agonists. This type of medication is growing in popularity and will soon be available via your GP on the NHS if you have certain conditions like high cholesterol, diabetes or other metabolic conditions. 

The weight loss drugs slow down how quickly food leaves your stomach, making you feel fuller for longer. They also reduce appetite and improve blood sugar control, which is why they’re used in type 2 diabetes as well as obesity.

But slowing down digestion may affect your gut.

How slower digestion affects your microbiome

These medications don’t just slow the stomach down – they can also reduce movement through the small intestine. This is important, because your small intestine relies on regular, rhythmic contractions (known as the migrating motor complex) to sweep away bacteria and undigested food between meals.

When food and waste sit in the small intestine for longer than they should, it creates an environment where bacteria can can overgrow.

Motility issues are a known factor in developing SIBO.

Weight loss drugs can also slow down bile production, which is an important part of small intestine motility and food breakdown. (In fact the GLP-1 drugs slowed bile flow so much they are emerging as a treatment for bile acid diarrhoea (read my blog for more about bile acid malabsorption)

What is SIBO?

SIBO stands for small intestinal bacterial overgrowth. It happens when bacteria start to build up in your small intestine causing bloating and excessive gas. 

The small intestine isn’t designed for this large number of bacteria. When you have too many microbes they can start to ferment carbohydrates from your food. They may also interfere with digestive enzyme production or bile acid malabsorption. 

These issues can lead to symptoms like:

• Bloating (especially after meals)
• Diarrhoea or constipation
• Excessive gas or frequent burping
• Nausea or feeling full quickly
• Abdominal pain or cramping

It’s estimated in people with IBS, SIBO may contribute to symptoms in around 38% of cases. 

Is there evidence linking weight loss injections and SIBO?

Because wide spread use of these weight loss drugs is quite new there aren’t many large studies. You can find growing reports of people developing SIBO-like symptoms while on GLP-1 medications. 

There is some research showing a link including:

• SIBO incidence – Case reports of diagnosed SIBO after starting semaglutide or tirzepatide
• Slowed motility – Studies showing slowed gut motility and increased bacterial overgrowth in healthy controls and patients with IBS.
• Gut symptoms – Studies indicate that nausea occurs in approximately 15-50% of users, vomiting in 5-20%, and constipation in 4-12% of people taking weight loss drugs. 

We already knew there was a link between diabetes, obesity and SIBO so it’s not unexpected to find a link between people who have SIBO in these populations.

Some people could have had digestive issues before starting their weight loss drugs that weren’t picked up or registered. 

The science of weight loss drugs and SIBO

However, a big recent study linked increased hydrogen SIBO diagnosis among obese patients using weight loss medications.

The study looked at over 1,400 people who had breath tests for SIBO and found that those using weight loss drugs, including GLP-1 medications like Wegovy or Mounjaro, were significantly more likely to test positive.

People taking GLP-1s were twice as likely to have hydrogen SIBO or intestinal methanogen overgrowth (IMO), a form of SIBO linked to constipation.

Some people tolerate these drugs very well. But for others, especially those with a sensitive digestive system, the impact on gut movement can be significant.

There are also reports of people becoming more sensitive to lactose after taking semaglutide due to SIBO.  

This growing mix of preclinical data, clinical observations, and patient anecdotes suggests that SIBO may be a significant, though underrecognised, side effect of GLP‑1 weight-loss treatments for some people.

If your gut symptoms develop or worsen on these medications, it’s worth investigating further.

Who might be more at risk?

You might be more likely to develop SIBO while on weight loss injections if you:

• Already have IBS or a history of constipation
• Have diabetes-related gastroparesis
• Have had SIBO before
• Have been on the medication for a long time or at a higher dose
• Don’t eat regularly or skip meals often (which reduces the natural gut-cleansing contractions)

What can you do if you suspect SIBO?

If your digestive symptoms have changed since starting a GLP-1 medication, it’s important not to ignore it. Here are some steps you can take:

• Speak to your GP or prescribing clinician before making any changes to your medication about the digestive symptoms.
• Get tested for SIBO—a lactulose breath test can help identify it. Read more about testing for SIBO in my blog post. 
• Support gut motility with regular meals, staying hydrated, gentle movement, and in some cases, specific supplements or prokinetic agents.
• Work with a practitioner who understands both your digestive health and the impact of these medications.

Don’t take weight loss medication unless it’s been prescribed by a doctor, buying it off the internet can be easy, but it’s not always suitable for everyone to take the medication.

Should you stop taking the injections?

Not necessarily. These drugs can be really helpful for many people. But if they’re causing uncomfortable gut symptoms, that doesn’t mean you have to just put up with it. You may be able to continue them with extra support for your digestion.

Improving your digestion alongside the medication can make huge changes to symptoms such as gas, bloating, nausea, and erratic bowel movements. Others may need more targeted treatment for SIBO alongside their weight loss plan.

Final thoughts

SIBO isn’t always easy to spot, especially when symptoms overlap with IBS. If you’ve started a GLP-1 medication and your digestion has changed, speak to your doctor about the symptoms. 

Supporting your gut AND managing your weight is possible. You don’t have to choose between one or the other.

Get in touch if you’d like to speak to me about working on your digestion in my 3 month Gut Reset programme.