I can't see some databases even though my user has the "root" role
This is because you have not restarted your MongoDB instance in auth mode. 
Restart your MongoDB in auth mode in linux like this

mongod --auth --fork --logpath /var/log/mongod.log


Reference: Enable Auth

Remember if you have enabled auth mode for your MongoDB instance, you must have put it in your code and start the mongod process in auth mode.  

To simplify this (authenticating the db) use Studio 3T (MongoDB Client) but you still need to start the instance with the --auth command line option.