In a Dutch oven over medium heat, melt the butter. Stir in the onion, carrot, and shallots. Reduce the heat to medium low and saute them until soft & tender- roughly 8-10 minutes.
Add the broth & flour to a large mixing bowl. Whisk until combined and no lumps remain. Pour this mixture into the Dutch oven, and stir to combine with the veggies.
To the pot add the seeds, half & half, salt, and pepper. Stir.
Raise the heat back to medium, and let the mixture simmer (stirring often) until thickened- about 5 minutes.
Reduce the heat to low, and stir in the cheese. Continue stirring until the cheese has melted and the soup's smooth, and do not let the mixture boil.
Slowly pour in the beer. Slowly, to reduce foaming, and stir the whole time you're pouring it in. Once the beer's incorporated, add the sausage.
Ladle into soup bowls and serve warm with rye bread.