There’s a good article from IBM about the five common PHP database problems users encounter when working with databases and php.

Some of the tips include refraining from directly access mysql php functions (this should be abstracted to a database layer, so you can swap out your database easily without having to modify the code).

Also it talks about the n+1 pattern, in which the app retrieves a list of items, then cycles through each item and grabs the relevant info for each item. In a small database, this is not a problem, but with over 1,000 records, that’s 1,000 more database queries to retrieve the info.

A lot of this recurring can be solved with database relations and normalization.

It also recommends not using more than 1 database for an entire application.