Many people assume that if they’re having a bowel movement every day, their digestion must be working normally.

But bowel frequency only tells part of the story.

In clinic, I often see people who are opening their bowels daily yet still struggle with bloating, food sensitivities, reflux, abdominal discomfort or recurring SIBO. They may not consider themselves constipated, but their digestive system isn’t necessarily moving food efficiently.

For years we’ve been told that diet is the most important factor shaping the gut microbiome. Emerging research suggests another factor may be just as important: how quickly food moves through the digestive tract.

This is known as gut transit time.

For years, gut health conversations have focused almost entirely on food.

What should you eat? Which foods feed beneficial bacteria? Which foods should you avoid?

While nutrition remains important, emerging research suggests that transit time may play a surprisingly powerful role in shaping the gut ecosystem.

Transit Time May Be One of the Biggest Influences on Your Microbiome

A 2024 study published in Nature Microbiology identified gut transit time as one of the strongest factors associated with differences in the gut microbiome between individuals.

The researchers found that longer transit times were associated with increased methane production and greater protein fermentation within the colon.

This may help explain why two people can eat very similar diets yet have very different microbiome profiles.

It’s not just about what enters the digestive tract. It’s also about how long it remains there.

One of the most important drivers of healthy motility is the Migrating Motor Complex (MMC).

The MMC is a series of cleansing waves that sweep through the stomach and small intestine between meals. Its job is to clear away food residue, move bacteria downstream and reduce stagnation within the small intestine.

The MMC only activates when you’re not eating: every snack temporarily switches it off. This is one reason why constant grazing can sometimes contribute to digestive symptoms in susceptible individuals.

Poor motility is one of the major risk factors for Small Intestinal Bacterial Overgrowth (SIBO) and the relationship is often bidirectional. Poor motility can contribute to SIBO, while SIBO itself can further impair motility, making recurrence more likely if the underlying issue isn’t addressed.

This is particularly true when methane-producing organisms are involved.

Research consistently shows that methane is associated with slower intestinal transit and constipation. In fact, recent microbiome research has found that people with longer transit times tend to produce more methane.

Clinically, this creates a vicious cycle. As transit slows, methane production may increase. As methane increases, transit can slow further.

This may help explain why some people experience persistent bloating, constipation and recurring SIBO despite dietary changes alone.

It does mean that long-term avoidance without understanding the underlying cause can sometimes create new problems while trying to solve the original one.

Motility doesn’t operate in isolation. Healthy digestion also relies on adequate bile flow and digestive enzyme production.

Bile plays several important roles in digestion. It helps break down dietary fats, supports healthy bowel movements and influences the balance of microbes living within the gut. This means poor bile flow can contribute to bloating, sluggish digestion and constipation.

Digestive enzymes help break food into absorbable nutrients. When digestion is incomplete, more material reaches the colon where it can be fermented by bacteria, potentially contributing to gas, bloating and digestive discomfort.

Signs Your Motility May Not Be Optimal

Not everyone with poor motility is obviously constipated.

“Needing a coffee to ‘get things moving’ every morning may be a sign that your motility needs support.”

Kate Troup, Naturopath

The best way to improve motility depends on understanding why it has slowed in the first place.

In some people, the issue may be methane-dominant SIBO or another form of microbial overgrowth. In others, thyroid dysfunction, poor bile flow, low stomach acid, medication use or nervous system dysregulation may be contributing. Diet and lifestyle factors also play a role, including inadequate fibre intake, insufficient movement and prolonged periods of stress.

This is why simply taking a laxative rarely addresses the root cause. While it may increase bowel frequency, it doesn’t necessarily restore healthy digestive function or normal transit through the entire digestive tract.