The theme of a short story is essentially the way that a writer is able to communicate with the readers on a common ground. The theme can be different if the short story is meant to be a moral story or if the short story is one that is fictitious.
When a short story is presented as a fable, the theme of the short story is the moral that lies within the story. It is the ground by which the characters make their decisions and the way that the story ends. When a short story is one that is completely fiction, it is not preaching or teaching in the way that a short story fable would be. It is abstract and is the basis by which the characters make decisions and communicate within the story. It is the setting for the feelings the characters have and the reason why the choices are made throughout the story. In short stories that are nonfiction, the theme can be very abstract. The theme is never stated in true stories and is often evident only by the way that the characters act. The things that the characters do, the words they speak, the tone they use and the setting they are in make up the theme of the short story.