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We propose a scheme for implementing quantum gates for two atoms trapped in distant cavities connected by an optical fiber. The effective long-distance coupling between the two distributed qubits is achieved without excitation and transportation of photons through the optical fiber. Since the cavity modes and fiber mode are never populated and the atoms undergo no transitions, the gate operation is insensitive to the decoherence effect when the thermal photons in the environment are negligible. The scheme opens promising perspectives for networking quantum information processors and implementing distributed and scalable quantum computation.