Kitum Cave in Kenya used to be a lot smaller than it is, but over hundreds of years it has been dug out deeper and deeper. In theory, the excavators turned out to be area elephants; along with other mammals the pachyderms gather in the cave to partake of its natural saltlick properties. In the process, they have been using their tusks to scrape and remove the cave's walls throughout time. Atlas Obscura has the story, along with another piece of trivia.
The Kitum cave is more recently famous for a very different sort of lifeform, a deadly virus. In 1980 and again in 1987 visitors to the cave contracted Marburg virus, a deadly virus very similar to Ebola. The cave and Marburg virus rose to notoriety when it was featured in bestseller "The Hot Zone." It is believed that the bats in the cave may carry the virus and that their powdered guano may act as the disease vector.