When you eat a chili pepper, a substance called capsaicin gives you that hot, spicy sensation. Capsaicin is so potent that it's even used in anti-bear sprays. However, far from irritating the stomach, as you might expect, some evidence suggests that capsaicin can help with digestion. This includes signaling the stomach to release more substances used in digesting foods.
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In the book "Modern Alkaloids: Structure, Isolation, Synthesis and Biology," the authors point out that capsaicin can stimulate stomach activity. In particular, capsaicin might signal the stomach to produce more gastric mucus. This helps with the digestion process. In that respect, capsaicin acts as a digestive aid -- speeding up the process. This backs up suggestions that capsaicin also speeds up metabolism slightly, increasing rates of digestion and energy use in the body.
A 2009 article from NYU's Langone Medical Center suggests that in addition to stimulating digestive enzymes, capsaicin might also fight harmful gut bacteria. In some cases, this bacteria can cause infections or lead to diarrhea, which interferes with the digestive process by loosening stools to the point where they pass through the bowel as liquid. This removes fluids and electrolytes from the body not normally removed during digestion.
Capsaicin might also play a role in curbing your appetite. Scientists from Purdue University found that hot red pepper helped suppress appetite, particularly in people who don't usually eat the substance. Participants reported less hunger for sweet, fatty and salty foods. This lack of urge to eat might reduce pressure on your digestive system. Fatty and high-sugar foods can irritate the gut or cause constipation.
As of July 2011, some evidence points to a link between the consumption of fresh red pepper and some types of stomach cancer. However, this evidence is inconclusive and contradicted by other reports of anti-cancer properties in capsaicin, though it might irritate mouth ulcers or existing esophageal problems such as those triggered by GERD. This can interfere with the digestive process by causing acid reflux or pain in the chest.