wordpress in a educational institution

We are a group of developers students at a university and we are grabbing a system where we are going to implement wordpress for each course, our little problem is that we have approximately 1000 subjects and we need 1000 blogs, in a matter of the database would have to use an database for all blogs, shared, and the problem is that each blog uses its own database. This will represent a problem at the server? We were chatting with a consultant and said it is a big problem, I would like to know if someone implemented at this level, if we can give suggestions or a small support
Many thanks in advance.
Atte developers at the University of Sonora