I interpret the phrase simply to mean, "the kernel, as opposed to the many other layers of software that are wrapped around it."
"The kernel" of an operating-system is the central "system control program" that actually operates the hardware of the machine. The kernel is loaded into memory at boot-time, and it stays there. (In Linux, the kernel also includes loadable kernel modules, which function as part of the kernel when loaded.)
Most programs never deal directly with the kernel: they use shared libraries such as glibc to do nearly everything.