The hybridization of distinct quantum systems is now seen as an effective way to engineer the properties of an entire system leading to applications in quantum metamaterials, quantumsimulation, and quantum metrology. One well known example is superconducting circuits coupled to ensembles of microscopic natural atoms. In such cases, the properties of the individual atom are intrinsic, and so are unchangeable. However, current technology allows us to fabricate large ensembles of macroscopic artificial atoms such as superconducting flux qubits, where we can really tailor and control the properties of individual qubits. Here, we demonstrate coherent coupling between a microwave resonator and several thousand superconducting flux qubits, where we observe a large dispersive frequency shift in the spectrum of 250 MHz induced by collective behavior. These results represent the largest number of coupled superconducting qubits realized so far. Our approach shows that it is now possible to engineer the properties of the ensemble, opening up the way for the controlled exploration of the quantum many-body system.