The Brood
The Brood use a virus that effectively lobotomizes the creatures, then they use bionics to control them. The Brood hollow out part of the creatures (by eating them) and use the space created to live in, like termites eating a tree. This eventually kills the living ships, requiring them to capture new ones. One of the Acanti they captured was of unusual size (its rib cage alone was the size of a mountain range.) They used it as their main base, and, when it died and crashed onto a planet, used it as their main city. The corpse was so large, it took centuries just to rot halfway. However, predators from the planet they landed on infested the area of the dead Acanti's brain, so the Brood avoided it.