Holes in your poop are almost always caused by gas bubbles that got trapped inside the stool as it formed in your colon. Bacteria in your large intestine ferment undigested food, producing hydrogen, carbon dioxide, and methane. Some of that gas escapes as flatulence, but some gets locked inside the stool itself, leaving behind visible pockets, tunnels, or a sponge-like texture once you pass it. In most cases, this is completely normal and not a sign of disease.
That said, the amount of gas trapped in your stool can vary depending on what you ate, how your gut bacteria are behaving, and whether your body is absorbing nutrients properly. When the holes are frequent, large, or paired with other changes in your stool, it can point to something worth paying attention to.
How Gut Bacteria Create Gas Pockets
Your colon houses the densest concentration of microbes in your entire body, and their primary job is fermenting whatever your small intestine didn’t fully break down. Poorly digested carbohydrates are the main fuel source. When bacteria in genera like Bacteroides ferment these carbohydrates, they produce hydrogen and carbon dioxide. Other specialized microbes then consume that free hydrogen to produce methane or hydrogen sulfide. All of these gases can become embedded in stool as it solidifies during its journey through the colon.
Research in mice and humans has confirmed that the gas content of stool is directly linked to microbial colonization. A classic study using floating and sinking stool samples from healthy volunteers found that buoyancy was primarily determined by how much gas was trapped inside, not by fat content as many people assume. Odorless methane is one of the biggest contributors. So if your poop has visible holes and also floats, that’s a strong sign the holes are simply gas pockets, and it’s a normal byproduct of a functioning gut microbiome.
Foods That Increase Gas in Stool
Certain foods are far more likely to feed gas-producing bacteria. High-fiber vegetables like broccoli, cauliflower, cabbage, and Brussels sprouts are common culprits. Beans, lentils, and whole grains contain complex carbohydrates that resist digestion in the small intestine, arriving in the colon mostly intact for bacteria to ferment. Dairy products cause excess gas if you’re lactose intolerant, because undigested lactose becomes fuel for fermentation. Sugar alcohols found in sugar-free gum and candy (like sorbitol and xylitol) have the same effect.
If you notice holes in your stool after eating these foods, there’s nothing abnormal happening. Your gut bacteria are simply doing their job with the material they were given. The holes may come and go depending on your diet from day to day.
When Gas Production Becomes Excessive
Sometimes the gas isn’t just from last night’s dinner. Small intestinal bacterial overgrowth, often called SIBO, occurs when bacteria that normally live in the colon migrate into the small intestine and begin fermenting food much earlier in the digestive process. The result is excessive gas accumulation, bloating, abdominal cramps, and changes in bowel habits. About two-thirds of people with SIBO report distension and flatulence as their primary symptoms.
When the overgrowth involves methane-producing organisms like Methanobrevibacter smithii, constipation tends to dominate. When hydrogen-producing bacteria are the main players, diarrhea is more common. Either pattern can produce stool with more gas pockets than usual. SIBO is diagnosed with a breath test that measures hydrogen and methane levels after you drink a sugar solution. A hydrogen spike of at least 20 parts per million above baseline within 90 minutes, or methane above 10 parts per million at any point, suggests overgrowth.
Fat Malabsorption and Porous Stool
Holes in stool don’t always come from gas alone. When your body can’t properly absorb fat, undigested fat passes into the colon, where it changes the texture and consistency of your stool. This condition, called steatorrhea, produces stools that are bulky, pale or clay-colored, loose, oily, and foul-smelling. They tend to float and can be difficult to flush. The greasy, irregular texture can sometimes look pitted or porous.
Several conditions cause fat malabsorption. Exocrine pancreatic insufficiency means your pancreas doesn’t produce enough digestive enzymes to break down fat normally. People with this condition pass significantly more fat in their stool than average, giving it that characteristic greasy, pale appearance. Celiac disease damages the lining of the small intestine, reducing its ability to absorb nutrients including fat. Stanford Health Care describes celiac-related stools as bulky, loose, pale, frothy, and foul-smelling. The “frothy” quality comes from a combination of trapped gas and unabsorbed fat, both products of incomplete digestion.
Parasitic infections can produce similar changes. Giardia, a waterborne parasite, causes greasy, smelly stool that floats, along with gas, stomach cramps, and diarrhea. If you’ve recently traveled or been exposed to untreated water and your stool looks different, a Giardia infection is worth considering.
Normal Holes vs. Something Worth Investigating
Occasional holes or air pockets in otherwise brown, well-formed stool are normal. You ate something fibrous, your gut bacteria produced gas, and some of it got trapped. No action needed.
The picture changes when holes or a porous texture show up alongside other symptoms. Pay attention if your stool is consistently:
- Pale, clay-colored, or greasy: suggests fat isn’t being absorbed properly
- Frothy or foamy: points toward malabsorption from celiac disease or similar conditions
- Accompanied by persistent bloating and cramps: could indicate SIBO or food intolerance
- Paired with unintentional weight loss: a red flag that nutrients aren’t being absorbed
Other warning signs that warrant medical evaluation include rectal bleeding, iron-deficiency anemia, and new digestive symptoms appearing for the first time after age 50. Persistent, unexplained changes in stool that don’t respond to dietary adjustments are also worth bringing up with a doctor, who can run targeted tests for malabsorption, bacterial overgrowth, or parasitic infection.
Simple Ways to Reduce Gas in Stool
If the holes bother you or come with uncomfortable bloating, a few dietary adjustments can make a noticeable difference. Reducing your intake of gas-producing foods for a week or two can help you identify the main triggers. Introducing high-fiber foods gradually rather than all at once gives your gut bacteria time to adjust without producing as much gas. Eating more slowly and chewing thoroughly reduces the amount of air you swallow, which also contributes to intestinal gas.
Cutting back on carbonated drinks, sugar alcohols, and dairy (if you’re lactose intolerant) addresses three of the most common non-fiber causes of excess gas. If these changes don’t help and you’re still seeing pronounced holes along with bloating, cramping, or changes in stool color and consistency, that’s useful information to bring to a healthcare provider who can look into malabsorption or bacterial overgrowth as underlying causes.