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Niobium is the material of choice for making the superconducting radio frequency cavities used in present-day accelerators for the acceleration of charged particles. In order to achieve high accelerating gradients for future accelerators such as the linear collider, thermal limitations in Nb cavities play an important role. The effects of plastic deformations due to applied strains on thermal conductivity of Nb in phonon transmission regime as well as on its Kapitza conductance have been studied. The study reveals absence of the phonon peak due to applied strains beyond the elastic limits of the Nb metal as well as reduced Kapitza conductance. This resulted in almost 80% reduction in thermal conductivity of the niobium at 2 K. Low temperature annealing did not recover the phonon peak as was seen before the application of plastic deformations.