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While observing the giant space amoeba discovered in 2268, Doctor Leonard McCoy described it as a very simple form of life capable of displaying almost all the functions living organisms perform, including the ability to breathe, eat and reproduce. (TOS: "The Immunity Syndrome")
For most humanoids breathing involves the intake of oxygen (respiration) and the exhale of carbon dioxide, to and from the lungs. The inability to breathe is known as suffocation. The predecessors of the Aquans, known to their descendants as "air-breathers", developed technology, a surgo-op process, that allowed their species to mutate into "water-breathers". (TAS: "The Ambergris Element")
Not all humanoids breathed the same, for example:
- The Axanar breathed nitrogen-methane. (ENT: "Fight or Flight")
- Benzites wore a respiration device in order to breathe in an oxygen-nitrogen environment. (TNG: "Coming of Age", "A Matter Of Honor")
- Lorillians, prior to the age of four, were only able to breathe methyl oxide. (ENT: "Broken Bow")
- Lothra breathed hydrogen. (DS9: "Melora")
- Yalosians breathed a corrosive mixture of 60% nitrogen, 10% benzene, and 30% hydrogen fluoride. (DS9: "Improbable Cause")
- Zaranites breathed fluorine and could not survive in oxygen, requiring them to wear breathing masks in class M environments. (Star Trek: The Motion Picture)