Doxy Jekyll theme comes with Disqus comments enabled by default with themeix profile information. You need to change the shortname to use your own discuss comment system.
Open _includes/disqus_comment.html file, and change the doxyjekyll value on line number 15 with your Disqus account shortname.
s.src = ‘//doxyjekyll.disqus.com/embed.js’;
So, if your Disqus shortname is example, the final code above should be
s.src = ‘//example.disqus.com/embed.js’;
That’s all you need to setup Disqus from the theme side. If you get any issue feel free contact us.