The phrase "is at the bottom of" is often used to describe something negative or a problem that needs to be addressed. There are several synonyms for this phrase that can be used to convey a similar meaning. For example, "lies at the root of" implies that the issue is deep-seated and fundamental. "Underlies" suggests that the problem is hidden beneath the surface. "Is the cause of" indicates that the issue is responsible for the negative outcome. "Is the foundation of" implies that the problem is so crucial that it serves as the basis for everything else. All these synonyms for "is at the bottom of" can add depth and precision to your writing.