Any bacteria that might be removed is not going to matter. The bacteria live on each and every surface in the tank, and in the filter. The amount that may be "sucked up" by the gravel vac is minimal, at best. Also, unless you are using an exceptionally powerful vacuum, the only way to remove a significant amount of the bacteria is to remove the gravel. Common gravel vacs and the Python are not nearly powerful enough to remove healthy bacteria from your gravel.
\Dan