Heat the pumpkin puree on medium-high heat until it starts to boil, about 5 minutes.
Add the kefir, cream, salt, and fresh-grated nutmeg to pumpkin. Simmer another 10 minutes. Let mixture cool 10 minutes.
Remove yolk from one of the eggs, discarding the white or using for another purpose.
Add yolk and other eggs, and brown sugar to a bowl and mix until smooth.
Add the sugar/egg mixture to the puree and mix well together.
Pull out middle oven rack halfway, and place crust on rack. Pour the custard mixture into the pan, and carefully slide the rack back into oven.
If using pomegranate, after 25 minutes of baking, sprinkle pomegranate seeds over the top of the pie.
Bake 40 minutes, or until the sides of the pie are firm but the middle is still jiggly.
Remove pie from oven and let cool at least 2 hours.