I'm a molecular biologist; I don't really have any formal training in microbiology. The Real Doctor has long pointed this out, noting that she's even done Gram stains, while I haven't even done this basic rite of micro.
Well, that situation has been fixed. Here's Bacillus subtilis, a Gram positive cell. The cells are nice and purple, so they've picked up and retained the Gram stain.
And here's Escherichia coli, a Gram negative. The Gram stain has leaked out of the cells (as it is supposed to), leaving only a pale safranin counter-stain.
The TA who is in charge of grading the section says that I passed.
Having approached microbiology from a molecular point of view, I've always been puzzled by the insistence on Gram staining as a method of identifying organisms. The first thing they teach you in micro lab is how to do a Gram stain; the first step in almost every dichotomous tree for identifying a sample is a Gram stain. Here's a portion--only a portion--of the "family tree" of all the Bacteria. I've highlighted the Gram positive group. All the rest are Gram negative.
Making "Is it Gram positive" your first question in identifying a bacterium is like trying to guess the identity of a human and making your first question "is the person an Eskimo?"