Walnut Levain from Runner & Stone, Brooklyn, NYC (Credit: Mayumi Kasuga)

No one really knows why celiac disease, an autoimmune disorder of the small intestine that's caused by eating gluten, and gluten sensitivities are on the rise. But celiac disease researchers and plant geneticists have some solid theories, one of which is the abbreviated fermentation times used at industrial bakeries.

"Most of the plastic-wrap bread you find at grocery stores is made very quickly with yeast--it goes from flour to plastic-wrap in three hours or less," says Stephen Jones, a wheat breeder who is the director of the Washington State University Research Center at Mount Vernon.

What that means is that gluten proteins don't have time to break down as they would in a bread made by traditional methods, where fermentation takes place over 18 to 25 hours, and that makes it harder to digest. It's possible, celiac experts theorize, that after years of eating highly processed bread, our guts are rejecting it.

Thankfully, there's a resurgence of craft bakeries around the country that make bread the old-fashioned way. All of these bakeries ferment their dough with wild yeasts for at least 12-15 hours--often much longer. This not only improves the digestibility of the bread but also lowers its glycemic index. All of these bakers also use "whole-milled" whole wheat flour--that is, flour that's been milled from its intact state. (To make white flour, industrial mills separate the endosperm from the more nutritious bran and germ. They add them back for whole wheat flour, but some craft bakers speculate that the germ, which goes rancid quickly when removed from the endosperm, is either not added back or is "denatured.") Some of these bakers even mill their own whole wheat flour in-house.

And perhaps most important of all: These breads taste fantastic!

Grand Central Bakery: This Northwest bakery, with ten locations in Seattle and Portland, ferments loaves for at least 12 hours. Portland head baker Sean Coyne, a Per Se alumnus, just launched a 100 percent whole-grain bread made from whole-milled whole wheat, emmer, spelt, and rye flours. The lighter Goldendale loaf (made with 68 percent whole wheat) is perfect for sandwiches. All the whole grain flours are milled at Camas Country Mill in Eugene, OR.

Ponsford's Place (San Rafael, CA): Unlike most bakers, Craig Ponsford uses 100 percent whole-wheat flour for all his breads--even the challah, which is made of hard white whole wheat. (His croissants and pain au chocolat are made of a whole-milled whole wheat flour that has 5 percent of the bran sifted off.) All the flour--used for loaves such as American whole wheat, sourdough walnut, and pumpernickel--has been whole-milled at Certified Foods in Woodland, CA.