Do you have children? Are you certain that something has not lodged inside the coiled piping within the comode base? have you run a snake through the comode base recently? Are you on a slab or pier and beam?
If the above has been checked out and is ok, then you have a problem from the toiled union to the drain and then on to the main line.
I hope that you do not have cast iron ground plumbing. this does rot out in 30 to 35 years. Then you are allowing mud and debris to constrict the pipe lining and act like chlosterol in the arteries thus not allowing a proper flush. You could also have tree roots penetrated into the line and caused a constriction.
What you need to do first, is to have a plumber come out and find the cleanout for that area and run his tree root sawing and debris moving snake into the lines to the main and clean out the junk.
What you need to do secondly is to call out a plumber that works with a snake with a camera on it and attached to a monitor and view inside your pipes to see what is happening.
I am very knowledgable on this right now unfortunately, because, I just had my entire plumbing, cast iron, replaced in my house. I have a slab home, 33 years old and the complete system was replaced via tunnels under my home and trenches in my yard. This was a huge $25,000 expense. I sure hope that this is not the case for you.