Persistent bad breath (halitosis) that doesn't improve with brushing, flossing, or mouthwash often originates from gut problems, not your mouth. When digestion is slow or bacteria are overgrown in your small intestine, foul-smelling gases travel upward. SIBO, H. pylori infection, and poor stomach acid production all cause bad breath from below. If your dentist can't find an oral cause, look at your gut.