Leave root and 1-inch stem on beets; scrub with a brush. Place in a medium saucepan; cover with water. Bring to a boil. Cover, reduce heat, and simmer 35 minutes or until tender. Drain and rinse with cold water. Drain; cool. Trim off beet roots; rub off skins. Combine beets and 2 tablespoons juice in a food processor; process until smooth. Set aside.
Position oven rack to lowest setting, and remove the middle rack. Preheat oven to 425°.
Place bread in a food processor, and process until finely ground. Lightly coat 8 (8-ounce) soufflé dishes with cooking spray. Sprinkle evenly with crumbs. Set dishes aside.
Lightly spoon flour into a dry measuring cup; level with a knife. Combine flour and 1/2 teaspoon salt in a medium saucepan over medium-high heat. Gradually add milk, stirring constantly with a whisk; bring to a boil. Cook 2 minutes, stirring constantly. Remove from heat. Transfer mixture to a large bowl; cool to room temperature. Stir in beet mixture and egg yolks.
Place egg whites in a large mixing bowl; beat at high speed with a mixer until soft peaks form. Add sugar, 1 tablespoon at a time, beating until stiff peaks form (do not overbeat). Gently fold one-fourth of egg white mixture into beet mixture; gently fold in remaining egg white mixture. Gently spoon mixture into prepared dishes. Sharply tap dishes on counter 2 or 3 times to level. Place dishes on a baking sheet; place baking sheet on the bottom rack of a 425° oven. Immediately reduce oven temperature to 350° (do not remove soufflés from oven). Bake 40 minutes or until a wooden pick inserted in the side of soufflé comes out clean.
Combine remaining 1 tablespoon juice, remaining 1/4 teaspoon salt, crème fraîche, and horseradish, stirring well with a whisk. Serve with soufflés.