(covers information from several alternate timelines)
Feces, also colloquially known as poo, poop, droppings, dung, or manure, was the product expelled from a being's digestive tract, consisting of bodily wastes.
In advanced civilizations, bodily waste was deposited in a toilet sent to the waste extraction system, where, after various processes, it would be recycled through biomatter resequencing. For infants, feces was often collected in a diaper.
According to Doctor Phlox in 2151, Altarian marsupial droppings contained the greatest concentration of regenerative enzymes found anywhere. Jonathan Archer found the idea of using droppings for regenerative purposes quite unusual when informed. However, Phlox reminded him that, if he was going to try to embrace new worlds, he must also try to embrace new ideas. (ENT: "Broken Bow")
When Miss Malvin's fourth grade class from Worley Elementary School in County Kerry, Ireland sent letters to Enterprise NX-01 later that year, Molly McCook wanted to know "When you flush the toilet, where does it go?" After Captain Archer passed the question to Commander Tucker, he responded with: "A poop question, sir?!" (ENT: "Breaking the Ice")
Bodily waste collected and used for agricultural purposes in the form of fertilizer, typically called manure, consists of high levels of methane. Kathryn Janeway recognized this upon detecting methane on a truck found in 2371. (VOY: "The 37's")
Some use the term "manure" as a metaphor for purposes of making a derogatory comment. The Species 8472 recreation of Boothby once referred to the Federation's concepts of "tolerance for all species" and the Prime Directive as "Targ manure." (VOY: "In the Flesh") Similarly, the slang terms "shit" and "bullshit" were slang terms of profanity that referred to the manure in general and that produced by a bull, respectively. The cursing "Merde" (meaning "shit") was also used in French language. (TNG: "The Last Outpost", "Elementary, Dear Data", Star Trek Generations; Star Trek: First Contact; Star Trek)
Another similar term, in the English language, was "crap." In 2263 of the alternate reality, Dr. Leonard McCoy told his friend and commanding officer James T. Kirk, who had just returned to the USS Enterprise following a disastrous away mission to the planet Teenax, that he looked "like crap," a comment Kirk sarcastically thanked him for. (Star Trek Beyond)
In addition to metaphoric usages, the idiomatic usage of the term "poop", as in "party pooper", refers to someone that is a killjoy. In 2372, the Little Woman referred to the Clown as a poop because he started feeling sorry for himself. (VOY: "The Thaw") While investigating a proto-nebula in 2375, The Doctor made an offhand comment about the Borg being the "party poopers of the galaxy", after Seven of Nine discouraged his attempt to use his holo-imaging device, and subsequently offered to begin a new social exercise with Seven to develop her joie de vivre. (VOY: "Drone")
In 3189, Admiral Vance remarked about the food security of replicator technology. By recycling their "Shit" the bio-matter produces food.