After a while, your MySQL databases will be fragmented, and you need to run the MySQL optimization to defrag it. A guy name Phil Dufault had written a shell script which can find all the fragmented tables in your databases and defrag them for you:
The author's repo: https://github.com/pdufault/mysqlfragfinder
Create a crontab to run that script periodically on a given schedule. For example:
# crontab -e
22 4 * * 0 /usr/local/bin/mysqlfragfinder.sh --user root --password mySuperPassword
That crontab will run the mysqlfragfinder.sh at 4:22 AM every Sunday.