The reason for these being created with root ownership in the first place is usually the way sudo
preserves some user environment.
ls: cannot access .gvfs: Permission denied
That folder .dbus
and .cache
with all it contents is supposed to be owned by the user whom the home directory belongs to.
It is usually safe to delete either, it will be recreated next time you login (it is just a cache that would have gone obsolete eventually).
# be careful what you type when you use rm -rf!
sudo rm -rf ~/.dbus
Keep in mind that .gvfs
behaves somewhat special since it's a mount point (check the output of mount
to confirm). As long as you have network folders mounted, don't touch it.
~/.cache/dconf
and~/.gvfs
owned by root. Could this be from running nautilus as root?