Already on December 16th, 2012, I predicted that nothing good can come from Microsoft's taking over Skype. Now my prediction came true. German IT News Agency Heise Online has proven that Microsoft doesn't only record all Skype chats. They actively use the data and seem especially interested in confidential information like encrypted sites, cloud storage and access codes.
In tests, especially set up testservers have been visited by Microsoft machines shortly after a link was transmitted in a Skype chat. The Microsoft scanner even used access codes if those were transmitted too.
DO NOT under any circumstances use Skype for any business-related or otherwise sensitive communication!
Consider not using Microsoft products at all anymore. If they already do it in Skype, who knows what they do if you run Windows and they have control over your whole computer or phone?