Clathrates can form a type of guest-host solid structures that, unlike most crystalline solids, have very low thermal conductivity. It is generally thought that the guest atoms caged inside the host framework act as "rattlers" and induce lattice dynamics disorders responsible for the small thermal conductivity. We performed a systematic study of the lattice dynamical properties of type-VIII clathrates with alkali and alkaline-earth guests, i.e., X8Si46 (X=Na, K, Rb, Cs, Ca, Sr, and Ba). The energy dependent participation ratio (PR) and the atomic participation ratio of phonon modes extracted from density functional theory calculations revealed that the rattler concept is not adequate to describe the effect of fillers as they manifest strong hybridization with the framework. For the case of heavy fillers, such as Rb, Sr, Cs, and Ba, a phonon band gap was formed between the acoustic and optical branches. The calculated PR indicated that the fillers suppress the acoustic phonon modes and change the energy transport mechanism from propagative to diffusive or localized resulting in "phonon-glass" characteristics. This effect is stronger for the heavy fillers. Furthermore, in all cases, the guest insertion depressed the phonon bandwidth, reduced the Debye temperature, and reduced the phonon group velocity, all of which should lead to reduction of the thermal conductivity.