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Breathing was a physiological process of gas exchange that remains one of the primary qualifiers that describe a living organism.

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")

A low respiratory rate was one of an injured Pavel Chekov's symptoms in 1986. (Star Trek IV: The Voyage Home)

Some individuals stopped breathing while they slept. In 2372, Quark explained that he used an eavesdropping device to monitor a sleeping Rom, who sometimes stopped breathing during sleep. Odo didn't believe him. (DS9: "Crossfire")

Not all humanoids breathed the same substances, for example:

A one-word instruction to "breathe", which T'Pol says to Tucker at the end of a neuro-pressure scene in ENT: "Similitude", wasn't scripted.

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