This paper describes our findings regarding the accumulation of motile bacteria at the rear of a confined obstacle and the physical description of the mechanisms at play. We found that the modification of flow due to the presence of the obstacle produces vorticity that favor the diffusion of bacteria towards the downstream stagnation point. By testing different flow rates, we determined the range in which bacteria accumulate. More interestingly, we observe that hydrodynamic interaction between the bacteria and the top and bottom surface of the microfluidic chip maintain the bacteria in the region where the flow velocity is lower than their own velocity. In the case of non-motile bacteria, this effect is not observed because bacteria follow the streamlines as passive tracers do.