A bottle was a handheld container for the storage and transport of liquids. They could be made of different materials.
The sickbay aboard Enterprise NX-01 featured several bottles in different colors on its shelves. (ENT: "Terra Nova", "Breaking the Ice")
The Akaali apothecary Riaan kept several different sized bottles and jars in shelves in her apothecary shop filled with different liquids and powders. (ENT: "Civilization")
In 2153, archaeologist Drake told a contact aboard the transport Arctic One to contact Starfleet Command and inform Commander Williams that he owed him a bottle of scotch. (ENT: "Regeneration")
A thermos bottle often included a cup which was fitted atop the bottle. (ENT: "Regeneration")
Shuttlepods of the 22nd century typically included a bottle for urination. In 2153, Sim remarked to Jonathan Archer that one of the worst fates he could imagine involved having to "pee in a bottle" while "cooped up" in one of the shuttlepods during old age. (ENT: "Similitude")
In 2285, Doctor Leonard McCoy gave Admiral James T. Kirk a bottle of Romulan ale as gift for his birthday. (Star Trek II: The Wrath of Khan)
Perfume was often kept in small and decorative bottles. (TNG: "Aquiel")