A bee was a winged hive insect, native to Earth, which gathered nectar and pollen from flowers. Bees made honey and beeswax. (TNG: "A Fistful of Datas")
When Enterprise NX-01 was surrounded by several small Suliban cell ships in 2152, Commander Trip Tucker compared the vessels to a swarm of cloaked bees. (ENT: "Shockwave")
Doctor Leonard McCoy compared the sting of the flying parasites encountered on Deneva to the sting caused by a bee or a wasp, which also left their stinger in the wound. (TOS: "Operation -- Annihilate!")
The idiom "the birds and the bees" was meant to refer to courtship and sexual intercourse. When Captain Kirk and Commander Spock were discussing Vulcan mating rituals, Kirk remarked that there was no need to be embarrassed about it and that it would also happen to "the birds and the bees". Spock logically responded that "the birds and the bees are not Vulcans". (TOS: "Amok Time") Following the close encounter between Harry Kim and Derran Tal, they discussed the unexpected experience they shared, and despite their similar appearances on the surface, how different things were when it came down to the basics, "let's just say the birds and bees would be very confused." (VOY: "The Disease")
The children of the Starnes Exploration Party who were taken aboard the USS Enterprise pretended to be a swarm of bees, repeatedly exclaiming "bizzy" and threatening to sting the adults aboard the Enterprise. (TOS: "And the Children Shall Lead")