You want to optimize mysql tables from time to time in order to reduce fragmentation. Here’s an easy way to do it automatically (put it in a script and run it from cron for example)
What all those mean:
–all-databases, -A; Check all tables in all databases. This is the same as using the –databases option and naming all the databases on the command line.
–optimize, -o Optimize the tables.
-h host to optimize (you can skip if it’s the localhost)
-u mysql user
-p the password