What if your SIBO, IBS or Functional Dyspepsia isn’t about bacteria - but your Migrating Motor Complex (MMC)?

thegutremedy
Dec 31, 2025
5 min read

Updated: Jan 6

How your gut’s clean-up system affects motility, bloating and relapse

Text graphic reading ‘What if your SIBO, IBS or Functional Dyspepsia isn’t about bacteria – but your MMC?’ on a teal background.

If you’ve been told your SIBO, IBS or Functional Dyspepsia is caused by 'bacteria', it makes sense that everything you’ve tried has focused on killing, starving, or avoiding them.

Antibiotics.

Antimicrobials.

Restrictive diets.

But for many people, bacteria aren’t the main problem. They’re the symptom.

One of the most overlooked drivers of ongoing gut symptoms is something called the Migrating Motor Complex - or MMC. When it isn’t working properly, bacteria are given the perfect conditions to linger, no matter how carefully you eat or how many treatments you try.

What is the Migrating Motor Complex (MMC)?

The Migrating Motor Complex is a repeating pattern of muscle contractions that happens in your stomach and small intestine between meals.

Its job is not digestion. Its job is to clean-up.

The MMC:

Clears leftover food particles
Moves bacteria and debris out of the small intestine
Helps prevent bacteria from building up where they shouldn’t

This process has been well described in gastroenterology research and is considered one of the body’s main protective mechanisms against small intestinal bacterial overgrowth.

In very simple terms, it’s your gut’s cleaning cycle [1].

Illustration explaining the Migrating Motor Complex (MMC), showing wave-like contractions that clean the stomach and small intestine between meals.

When does the MMC fire?

This part is crucial - the MMC only works when you are not eating.

It:

Starts around 90–120 minutes after finishing a meal
Repeats in cycles while you remain fasted
Switches off as soon as you eat again
Can be suppressed even by small amounts of calories

This means:

Frequent snacking
Grazing throughout the day
Sugary drinks, milky coffees, or supplements between meals

…can all reduce how often the MMC gets a chance to do its job.

At night, when we naturally go longer without eating, the MMC usually becomes more active. This is one reason overnight gut movement is so important [2] [3] [4] [5] .

What does a working MMC feel like?

Some people clearly notice their MMC. Others don’t - and both can be normal.

Common signs it may be active include:

Gentle rumbling or gurgling sounds
A hollow or empty feeling in the stomach
Subtle movement sensations
Hunger that feels calm rather than urgent or shaky

These sounds are often labelled as 'loud digestion' [5].

In reality, they’re frequently a sign that things are moving as they should.

Why the MMC matters for SIBO

Impaired MMC function is one of the strongest known risk factors for SIBO [6].

Research has shown that:

People with SIBO have fewer and weaker MMC waves
Reduced MMC activity allows bacteria to remain in the small intestine
SIBO is far more likely to come back if MMC function isn’t restored

This explains a very common pattern:

Treatment helps temporarily
Symptoms improve, then return
Another round of treatment is needed

If the clean-up system isn’t working, the environment that allowed SIBO to develop hasn’t changed.

Why the MMC also matters for IBS and Functional Dyspepsia

MMC dysfunction doesn’t only affect SIBO [7] [8].

In IBS and Functional Dyspepsia, impaired gut movement can contribute to:

Food sitting in the stomach or upper gut
Prolonged fullness after meals
Upper abdominal pressure
Bloating that worsens between meals
Nausea not clearly linked to food quantity

In Functional Dyspepsia especially, coordination between the stomach and small intestine is often disrupted. When things don’t move on properly, symptoms can persist even when tests come back 'normal'.

This is why these conditions are described as functional - the issue is in how the system works, not what it looks like on a scan.

How does MMC dysfunction develop?

MMC dysfunction is rarely random and almost always has a root cause (which means that there's always things that can be done to help it!)

Common contributors include:

Chronic stress and nervous system dysregulation [1]

The MMC is tightly linked to the nervous system. Long-term fight-or-flight suppresses gut movement and prioritises survival over digestion.

Gut infections or food poisoning [9]

Post-infectious IBS and SIBO are well recognised. Certain infections can damage the nerves that control the MMC, leading to long-term motility issues.

Ongoing gut inflammation [10]

Inflammation interferes with normal muscle contractions and nerve signalling, making coordinated movement harder.

Restrictive eating or under-fuelling [11]

Long-term low calorie intake or fear-based restriction reduces the body’s incentive to prioritise motility.

Hormonal factors [12]

Thyroid imbalance, low oestrogen, and cortisol dysregulation can all slow gut movement.

Certain medications [13] [14] [15] [16]

Medications that can slow motility include opioid painkillers, proton pump inhibitors (such as omeprazole), medications with anticholinergic effects (including some antidepressants, antihistamines and bladder medications), Imodium (used for diarrhoea) and drugs that affect serotonin signalling, which can all reduce the strength or frequency of the Migrating Motor Complex in susceptible people.

Common medications including omeprazole, loperamide, antihistamines and opioid pain relief.

Structural or mechanical factors [17]

Adhesions, endometriosis, or abdominal surgery can physically interfere with normal gut movement.

Signs your MMC may not be working well

There is no single symptom that proves MMC dysfunction. Patterns are more important.

Common signs include:

Feeling full for hours after eating
Food feeling like it just 'sits'
Very little gut rumbling between meals
Bloating that worsens the longer it’s been since eating (this was my big tell-tale sign)
Symptoms worse overnight or first thing in the morning
Recurrent SIBO despite treatment
Nausea when meals are spaced further apart
Early satiety or loss of appetite

Person sitting at a table holding their stomach and feeling uncomfortably full after eating.

Some people also notice that eating temporarily relieves symptoms, which then worsen again later. This can be another clue that movement between meals is part of the issue [1] [5].

What can I do to help MMC function?

Prokinetics are substances that support or stimulate gut movement, including MMC activity [18]. They can be prescription or herbal, and both have been shown to be effective.

They:

Don’t kill bacteria
Don’t fix everything
Can help restore movement patterns when motility is impaired

They’re often considered:

After SIBO treatment
When symptoms keep relapsing
When signs point clearly to motility involvement

Prokinetics were a game changer for me, although it took a lot of trial and error to find the most effective one. There are different types, working in different ways, and context really matters. I cover this in much more detail here.

Practitioner perspective

Not everyone with SIBO, IBS or Functional Dyspepsia has MMC dysfunction.

But when symptoms persist, cycle, or return despite doing many things 'right', this system is very often part of the picture.

To sum up:

The Migrating Motor Complex (MMC) is your gut’s clean-up system, working between meals to keep the small intestine clear and coordinated.

When it isn’t functioning properly, bacteria linger, symptoms persist, and conditions like SIBO, IBS and Functional Dyspepsia are far more likely to become chronic or recurrent.

Clues like prolonged fullness, lack of gut movement between meals, and repeated relapse can all point towards MMC involvement. I had all of these symptoms and prokinetics really helped me move the dial.

If this resonates, your experience makes sense. And it often means there’s more going on than just bacteria or food.

References: