Bacteria is a precise term that has a scientific definition.
'Germs' has no scientific meaning. It's an everyday word that we use - in a very imprecise and general way - to mean 'invisible things that make us ill'. When we say 'germs' we are thinking about bacteria, but also other pathogens such as viruses. For example, in everyday ( non-scientific) contexts, we can talk about the cold and flu viruses being spread by 'germs'.