How do bacteria survive stomach acid?

Some bacteria are really tough. They have protective layers around them that enable them to survive acid. Some viruses actually need the acidic environment of your gut in order to infect you. Some bacteria, such as Clostridium perfringens, which causes gas gangrene, and Clostridium difficile (C.diff) form spores. These spores are tiny husks of dried up bacterium, almost in suspended animation, which can pass through the stomach without being damaged and they can come back to life in the relatively nice environment of the intestines.

Other bacteria, like Helicobacter pylori, which is linked to causing stomach ulcers and stomach cancer, encode an enzyme called urease. Urease breaks down urea which is found in low levels in all our tissues, into ammonia, which is alkaline and neutralises the acid around the bacteria.