In short, yes it can.
A respiratory illness associated with bat guano is called Histoplasmosis. It begins in the lungs but has also been known to attack other organs such as the eyes. It is contracted by inhaling the spores from the organism H. capsulatem that can grow on bat guano. People become at risk when the H. capsulatem (histoplasmosis spores) are aerosoled and inhaled due to disturbing (eg. sweeping) bat guano.