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Modern communications have moved away from point-to-point models to increasingly heterogeneous network models. In this article, we propose a novel controller-based protocol to deploy adaptive causal network coding in heterogeneous and highly-meshed communication networks. Specifically, we consider using Software-Defined-Network (SDN) as the main controller. We first present an architecture for the highly-meshed heterogeneous multi-source multi-destination networks that represents the practical communication networks encountered in the fifth generation of wireless networks (5G) and beyond. Next, we present a promising solution to deploy network coding over the new architecture. In fact, we investigate how to generalize adaptive and causal random linear network coding (AC-RLNC), proposed for multipath multi-hop (MP-MH) communication channels, to a protocol for the new multi-source multi-destination network architecture using controller. To this end, we present a modularized implementation of AC-RLNC solution where the modules work together in a distributed fashion and perform the AC-RLNC technology. We also present a new controller-based setting through which the network coding modules can communicate and can attain their required information. Finally, we briefly discuss how the proposed architecture and network coding solution provide a good opportunity for future technologies, e.g., distributed coded computation and storage, mmWave communication environments, and innovative and efficient security features.