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Natural nesting habitats for honey bees include caves, rock holes, and hollow trees. In warmer climates, they may make exposed hanging nests on occasion. Aerial combs have been exposed in members of various subgenera. The nest is made up of numerous honeycombs that run parallel to one another and have a very homogeneous bee area. It normally only has one entrance. Western honey bees prefer nest cavities with a volume of 45 liters or more, avoiding those with a volume of less than 10 liters or more than 100 liters.  Western honey bees have a few nest-site preferences: the height above ground is usually between 1 meter (3.3 ft) and 5 meters (16 ft), entrance positions tend to face downward, equatorial-facing entrances are favored, and nest sites are over 300 meters (980 ft) from the parent colony.  Bees typically stay in their nests for several years.

The bees often polish the bark around the nest entrance and coat the cavity walls with a thin layer of propolis, a hardened plant resin. Along the cavity tops and sides, honeycombs are linked to the walls, while minor passageways are left along the comb edges.  Honey is kept in the upper portion of the comb; beneath it, rows of pollen-storage cells, worker-brood cells, and drone-brood cells, in that order, make up the basic nest architecture of all honeybees. Normally, the peanut-shaped queen cells are formed towards the comb’s lower border.