The transport of suspension containing autopropelled particles is deeply modified by the presence of flow, boundaries and other particles. In particular, when an active suspension is flowing in confined domains, the geometry can condition and modify the shear that the particles experience, producing different effects on bacterial accumulation, thereby modifying the transport properties. During this talk, we will discuss a few experimental examples where the coupling geometry-flow will significantly affect the transport of bacterial suspensions. Experiments were conducted by flowing a diluted suspension of Escherichia coli through microchannels with different designs. The first set of experiments will study the accumulation of cells in regions with specific shear/flow velocity and the other set up will show how the shear can affect the accumulation or attachment of cells at the wall.