How Your Digestion Speed Affects Your Overall Health

The amount of time it takes for stool to travel through your body may influence your health in surprising ways.

A 2023 study found that the bacteria living in your gut can look very different depending on whether your digestion is fast or slow. The human gut microbiome is closely tied to overall health.

Slow digestion and constipation have been linked to metabolic and inflammatory conditions, as well as neurological diseases like Parkinson’s Disease. Researchers reviewed past studies on gut transit time, all aiming to figure out how long food stays in the colon.

The longer stool stays, the more time bacteria have to break it down. This process changes acidity in the gut and creates substances that can affect health.

The study showed that people with fast gut transit had very different microbiomes than people with slow transit. One way researchers estimate transit time is with the Bristol Stool Scale, a visual chart that sorts stool by texture. Hard, pellet-like stools usually mean slow transit. Watery or mushy stools often mean fast transit.

Transit time can also affect how your body responds to probiotics, supplements, and medications that interact with the gut.

“The gut is far more than a digestive organ — it is a finely tuned ecosystem whose balance underpins everything from immune function and metabolic health to neurological well-being and cancer risk,” said Dr. Ketan Thanki, a board certified colorectal surgeon at MemorialCare Todd Cancer Institute in Long Beach, CA.

Healthline spoke with Thanki to learn more about how poop transit time can affect health.

This interview has been lightly edited for length and clarity.

How does poop transit time affect gut health?

Thanki: Gut transit time is a major factor in what kind of bacteria live in your gut, how diverse they are, and how they work. Slower transit is linked to a shift away from healthy sugar fermentation — which produces helpful short-chain fatty acids (SCFAs) — and toward protein fermentation, which creates potentially harmful byproducts like ammonia and phenols.

This relationship works both ways: transit time decides which bacteria thrive, but the bacteria and their byproducts — including SCFAs and bile acids — also affect how fast the gut moves.

Why does poop transit time lead to inflammatory and metabolic disorders?

Thanki: When transit slows down, the good carbohydrates get used up before stool reaches the far end of the colon. Bacteria then switch from fermenting carbs into healthy SCFAs to fermenting proteins instead. This creates metabolites like ammonia, hydrogen sulfide, phenols, indoles, and branched-chain fatty acids. These are toxic to colon cells, can damage their DNA, cause cancer-causing mutations, and make the gut lining leaky — which leads to body-wide inflammation.

At the same time, more methane gas is produced, which slows the gut even more. Higher estrogen levels in the blood can raise the risk of cancers like breast cancer and throw off other hormone levels.

A lack of SCFAs also affects the body’s metabolism. SCFAs aren’t just fuel for colon cells. They also send signals to the liver to control glucose production, and they influence fat tissue, insulin sensitivity, and appetite hormones (GLP-1, PYY). When slow transit cuts down SCFA production, these signals weaken. This is especially important in diabetes and obesity, where slow stomach emptying and altered transit make blood sugar control and energy balance worse.

Finally, gut bacteria turn choline and carnitine from meat and eggs into TMA, which the liver then changes into TMAO — a substance linked to heart disease. The study notes this link to transit time hasn’t been fully proven yet, but it is a possible way that heart disease could get worse.

What are the long-term health risks of slow digestion and constipation?

Thanki: Long gut transit time is linked to several serious long-term health risks:

– Colorectal cancer

– Breast cancer

– Neurological diseases, including Parkinson’s and Alzheimer’s

– Heart and kidney disease

– Metabolic problems that contribute to diabetes and obesity

This makes gut transit time one of the most overlooked factors in long-term health.

Can slow digestion or constipation lead to colon cancer?

Thanki: Colorectal cancer is one of the most well-established and serious links to chronic constipation. Slow transit allows harmful bile acids to build up, which are directly toxic to colon cells. When you add the shift toward protein fermentation — which creates ammonia, phenols, and hydrogen sulfide that damage the gut lining and colon cell DNA — and the loss of protective butyrate (a SCFA), the colon environment becomes more dangerous over time. The far end of the colon, where protein fermentation is strongest and transit is slowest, is also where most colorectal tumors develop.

What are some ways to improve digestion?

Thanki: Eat plenty of fiber (aim for 35 grams a day), drink lots of water (64 to 80 ounces a day), and cut back on red and processed meats (3 servings of red meat a week, and processed meats only rarely). Get fiber from different sources like vegetables, seeds, and whole grains. Don’t be afraid to take a fiber supplement like psyllium husk. Probiotic foods like yogurt, kefir, kombucha, and sauerkraut can help restore gut bacteria, especially the sugar-fermenting kind. And exercise! Even 20 to 30 minutes of walking a day will help get your gut moving.

How is chronic constipation managed?

Thanki: Think beyond your diet. While food and water are major factors, constipation has many causes. Move your body regularly: Even a daily 20 to 30-minute walk can stimulate bowel activity. Don’t hold in bowel movements — ignoring the urge trains your bowel to live with constipation. Try lifestyle changes to manage stress and improve sleep, and reduce medications that might slow things down. These can all affect your nervous system and hormones, which in turn affect gut movement.

If these changes don’t work, see your doctor to rule out other issues like hypothyroidism, pelvic floor dysfunction, or a problem with the colon itself. If constipation lasts more than a few weeks despite lifestyle changes, there is likely something else going on. Listen to your body and get it checked out.

Can chronic diarrhea lead to long-term health issues?

Thanki: Chronic diarrhea speeds up gut transit so much that your body can’t absorb nutrients or ferment food properly. This can lead to a cascade of long-term problems, including:

– Malnutrition

– Vitamin and mineral deficiencies

– Osteoporosis

– Electrolyte imbalances

– Chronic dehydration

The constantly weakened gut barrier allows bacterial products to enter the bloodstream, causing low-grade inflammation linked to autoimmune conditions. At the same time, low SCFA production starves colon cells and further weakens the gut lining. Finally, issues like hemorrhoids, anal fissures, rectal prolapse, and skin rashes can all be made worse by chronic diarrhea.