What causes bad breath?  There are so many sources of oral and nonoral sources of halitosis that it becomes very difficult to determine the best treatment once good oral hygiene techniques are practiced.  This article addresses a great deal of possible causes, including gram-negative anaerobes on oral debris and dental plaque that devour sulfur-containing substrates, candidiasis, and tonsil stones (tonsilloliths), achalasia of the esophagus, and the treatments options for halitosis. If you have taken antibiotics for a long time, you may develop a Candida infection in the mouth. 

 http://dentalresource.org/topic48halitosis.htm