Question

Is pepper harmful to the GI tract?

Answer 1

No

Explanation:

Pepper can refer to many different types of plants, however I assume you are talking about the traditonal pepper of the Piperaceae family.

Humans have been eating pepper for centuries, and is probably the most well-known spice across the world. Pepper rarely causes any harm to the GI tract, and even when it does irritate the muscous membrane of the GI tract, it is a mild irritant. It is rare to be allergic to pepper, but it is possible. If you are taking medication, have heart burn or other illnesses which require the stoppage of inflammtory foods, consult with your doctor before eating pepper.
http://www.livestrong.com/article/507857-black-pepper-digestion/

On the contrary, black pepper has been shown to be quite beneficial for the digestive system, aiding in weight loss, digestion, respiration, diarrhea and more- see these articles for more.
https://www.organicfacts.net/health-benefits/herbs-and-spices/health-benefits-of-black-pepper.html

http://food.ndtv.com/opinions/black-pepper-benefits-more-than-just-a-spice-1238993

I hope I helped!