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(covers information from several alternate timelines)
A diagram of the Human torso depicting the location of the lungs including the bronchial tubes was stored in the USS Enterprise's library computer database. This database was accessed by the Talosians in 2254. (TOS: "The Cage")
Suliban lungs normally had three bronchial lobes, however, the genetically altered Suliban soldiers had five. They also had alveoli clusters, which had been modified to process different kinds of atmosphere. (ENT: "Broken Bow")
In 2371, both of Neelix's lungs were removed by a group of Vidiians. Unable to create artificial lungs, The Doctor had to use a blood-gas infuser, a cytoplasmic stimulator, and an isotropic restraint in combination with his newly-created holographic organ replacement in order to keep Neelix alive. Later, one of Kes' lungs was altered and transplanted into Neelix by the Vidiians. (VOY: "Phage")
In an alternate timeline experienced by the Voyager crew in 2374, The Doctor instructed Tom Paris to treat a crewmember with damaged lung tissue with inaprovaline. Eighty-six days later, Captain Kathryn Janeway ordered The Doctor to treat her with trioxin after the alveoli in her lungs were chemically burned. (VOY: "Year of Hell", "Year of Hell, Part II")
During the Hirogen's takeover of the USS Voyager in 2374, Seven of Nine received a punctured lung in a holodeck recreation of World War II. Later, another crewmember also suffered a punctured lung. (VOY: "The Killing Game", "The Killing Game, Part II")