Natural Science Forum / Physics / Optics / February 2006

Just to add to what Gregor said, most identification of bacterial
species relies on tests other then microscopy. You may use a microscopy,
coupled with specific stains, to looks at the shape/size of the
bacteria, sporulation, presence/absence of a capsule, etc.  But most of
the identification is via identification through tests using
bacteria-specific antibodies (ELISA's), or genetic tests (PCR), or tests
of metabolic characteristics (i.e. tests for anaerobic/aerobic
metabolism, ability to break down various sugars, motility tests, etc).

And even with this huge panel of assays it is still very difficult to
identify most species of bacteria.  Generally speaking, pathogenic
bacteria are easy to ID, but outside of that it's much more difficult.
And, as a general rule, if you cannot culture the bacteria you wont be
able to ID it.

Bryan