It's a great tool, but don't just apply advice blindly. It's guidance, not "this is the right thing to do", and some of the advice can harm as much much as help, because no one has size fits all (though I will found it to provide a excellent suggestions in general).
Use it, look at the suggestions, and use that as an excellent springboard for reading up on what and why, and see how it could apply to your database.
https://github.com/major/MySQLTuner-perl