What command should I run manually?
Installing the upgraded package often won't restart the service, meaning you're still running old code, and in the case of libraries, won't restart every process on the system that has loaded the library, meaning you're still running old code...
1. Updates to the kernel
2. Updates to system libraries which services depend on
For 1, if you run Ubuntu you now have canonical-livepatch: http://blog.dustinkirkland.com/2016/10/canonical-livepatch.h...2 remains a problem, and yes, if you're thinking openssl, that's a problem. But you can track what goes into /var/run/reboot-required.pkgs to see it's really not 99% of fixes we're streaming to you.
See http://askubuntu.com/questions/775504/does-unattended-upgrad... for a more complete discussion.
sudo apt update
sudo apt upgrade
See also:sudo apt-get install --only-upgrade <package_name>