In the trend of hybrid Artificial Intelligence (AI) techniques, Physic Informed Machine Learning has seen a growing interest. It operates mainly by imposing a data, learning or inductive bias with simulation data, Partial Differential Equations or equivariance and invariance properties. While these models have shown great success on tasks involving one physical domain such as fluid dynamics, existing methods still struggle on tasks with complex multi-physical and multi-domain phenomena. To address this challenge, we propose to leverage Bond Graphs, a multi-physics modeling approach together with Graph Neural Network. We thus propose Neural Bond Graph Encoder (NBgE), a model agnostic physical-informed encoder tailored for multi-physics systems. It provides an unified framework for any multi-physics informed AI with a graph encoder readable for any deep learning model. Our experiments on two challenging multi-domain physical systems - a Direct Current Motor and the Respiratory system - demonstrate the effectiveness of our approach on a multi-variate time series forecasting task.