The way lines snaked out the door of her Rockridge shop, you’d think there were no bagels to be found in Berkeley, California, when Emily Winston opened Boichik Bagels in December.

A great bagel, boiled then baked, chewy on the inside with a leathery crust, was once impossible to find here. As New York-area transplant Winston took things into her own hands, she ended up creating a bagel that outshines the benchmark. That’s because she uses superior flour — much of which is whole grain — and that translates not only to better flavor but higher quality.

Some of her whole wheat comes from Bob Klein, a neighborhood fixture who, with his wife Maggie, has run Oliveto, one of the East Bay’s best and best-known restaurants, for over 30 years. Klein started Community Grains as a passion project just over a decade ago, and it’s become his mission in life.

Community Grains contracts with farmers to grow heritage wheat locally, fairly, and sustainably. With that grain, the company makes flour, breads, and pasta — preserving all of the germ and bran, where a majority of the nutrients reside, most of which are lost in the production of white flour.

Klein also prioritizes transparency in every step of the harvest. This includes knowing the farmers — Paul Muller of Full Belly Farm in the Capay Valley and Fritz Durst of Fritz Durst Farming and Tule Farms in the Sacramento Valley — the seed sources, soil management practices, when grains were milled, how they’re stored, the protein levels, and industry analysis of the flour. This might be common among principled chicken or tomato growers, but it’s rare in flour, and could change the way we look at bread.

Klein believes we should eat more whole grain, and he’s probably right. The recent 2020 Dietary Guidelines for Americans strongly recommend that all Americans make half or more of their grains whole grains.

This is especially true in the Covid era: Whole wheat contains germ and bran that boost our immune system with nutrients like selenium and zinc. “Why not eat something that has four times the amount of zinc as the same product made with only white flour?” said Dr. David Killilea, a biochemist at the University of San Francisco Benioff Children’s Hospital and the Children’s Hospital Oakland Research Institute. While zinc isn’t a magic cure in warding off disease, studies show it can help. And zinc-times-four is only present in true whole wheat that hasn’t been roller milled, which leaves out most of what’s on grocery store shelves.

‘Why not eat something that has four times the amount of zinc as the same product made with only white flour?’

The process of roller milling, which began in the mid-19th century, led to separating wheat components and the dominance of white flour, which is supremely shelf-stable (it’s the germ that can go rancid), bland, and nutritionally bereft (which is why it’s often“fortified” or “enriched”).

Roller mills now produce a majority of the flour in the United States –which means the nutritious germ and bran are left behind, so that even “whole wheat” flour becomes, essentially, refined white flour. To get the “whole wheat-looking” flour on grocery shelves, some of the bran is added back in. But to call this “whole wheat” is a joke.

To get the ‘whole wheat-looking’ flour on grocery shelves, some of the bran is added back in. But to call this ‘whole wheat’ is a joke.

That not all “whole wheat” is equal was made clear by a new study out of the University of California, San Francisco, which looked at whole wheat in select commercial brands, including King Arthur and Gold Medal, compared to standard all-purpose white flour. The difference, when it comes to our health, could be significant.

“Wheat has a really good amount of the nutrients needed for human health,” said Killilea, the researcher who conducted the study (which was spearheaded by Michael Pollan almost a decade ago; he also helped bring the study to fruition.) Killilea offered a long list of vitamins that wheat can provide — unless it’s roller milled.

“Beyond the traditional nutrients, whole wheat also contains many bioactive components known to promote good health for us and our microbial tenants….” he said. “The important caveat is the ‘whole’ in whole wheat, though, since the production of refined wheat flour removes most of these healthy compounds,” he said.

The vitamins and minerals that are lost with the germ and bran during roller milling and separation — specifically, fiber, vitamin E, vitamin B6, magnesium, zinc, copper, and folate— are the very nutrients that are most lacking among people in the United States, according to the USDA Nutrient Database and the National Health and Nutrition Examination Survey. Americans are not deficient in protein and carbohydrates, which makes up refined white flour. And “enriched” flour only adds back four vitamins and one mineral, none of which are shortfall nutrients in the average American diet.

But as the study showed, white flour isn’t the only problem. Using wheat germ agglutinin, a protein only found in the germ tissue of wheat kernels, Killilea was able to correlate it with the percentage of whole wheat found in commercial mixtures of whole and refined white flours. The big picture results of the study found that several national-brand flours packaged as whole wheat contain as little as 60 percent whole wheat; national brand pastas contained as little as 10 percent of it. (Among those tested for the marker of germ, Community Grains had the highest, Bob’s Red Mill, which is stone ground, was close, while King Arthur was third.)

It doesn’t make much of a difference what blend of wheat happens to be in a bag, Killilea said. “We tested several common wheat varieties in the U.S. representing three major market classes (hard red spring, hard red winter, and hard white winter), but the wheat germ agglutinin content varied less than 25 percent,” he said.

“This is a breakthrough test,” Klein said. “But it’s only the beginning. We need to do more testing.”

Dr. Walter Willett of Harvard’s T.H. Chan School of Public Health concurred with the findings. “The germ contains many nutrients and phytochemicals, so having a substantial part of it missing is serious,” he said in an email. “ Like any reports, it will be important to reproduce these findings, but this seems quite straightforward and is likely to be correct.” He added that the “priority should be making the product as healthy as possible by keeping the original proportions, and having an honest product.”

‘Priority should be making the product as healthy as possible by keeping the original proportions, and having an honest product.’

Why is it OK that a bag of grocery store flour billed as whole wheat contains something other than whole wheat in almost half the bag in some cases? In the letter he wrote to the editorial staff of the Journal of Food Science last fall, Killilea reminded reviewers that the U.S. Food and Drug Administration “states that flour just needs 51 percent whole grain to be called whole wheat. For wheat-based foods, it is even more unclear, with insiders suggesting some whole wheat products may often contain little whole grain. Currently, there are no independent tests to determine the whole grain level in a wheat product.”

So what’s the rest of the stuff in that bag? The FDA does not suggest, let alone mandate, laboratory analysis of the output of the milling process, Klein noted on the Community Grains website. The consumer might know how flour is made, but not how much authentic whole wheat is in that bag of flour or bread from the grocery store.

Those who are all-in on behalf of true whole wheat are up against some obstacles. For one, to better understand how to buy flour, people have to refamiliarize themselves with grain — the language, the range of grains, where and how to buy it, and for what — since we’ve lost literacy surrounding a fundamental source of nutrition. With the help of forward-thinkers like Dr. Stephen Jones of The Bread Lab out of Washington State University — along with the flourishing of small-batch millers and bakers — it seems like we’re starting to make some headway, if not yet on a mass scale.

Real whole wheat would have to become more accessible to everyone, not just sold for more than a buck a pound to devotees with money. It would also take some convincing that it can taste as good or better than white flour and offers a similar chew and crust.

And perhaps most significant, it requires a cultural shift. Americans are not in love with whole wheat anything; generally it’s about as popular as steamed cabbage. Even in a progressive food community like the Bay Area, restaurants and bakeries that rely on whole wheat avoid mention on their menus.

Emily Winston is a case in point. Across the bay in San Francisco at The Mill, Josey Baker — an excellent bread baker who names his loaves “Adventure Bread,” or “Red, White, and Rye” — is also low key about calling attention to whole wheat in his breads.

Even Oliveto edited out mention of whole grain pasta from its dining menu last year while continuing to use it. As Oliveto’s former head chef said last year: “My biggest problem with it is it doesn’t move.”

In talking to Winston and Klein before Boichik Bagels opened, they addressed the image problem of whole grain. “Around here you would think, ‘I plan on touting this. This is 100-percent single-farm-sourced whole wheat flour,’” Winston said. But Klein shrugged it off. “I think there are people who respond to that and others who respond to how it tastes.”

New and revived varieties of wheat have been introduced through The Bread Lab, Community Grains, and elsewhere, exposing millers, bakers, and consumers to true whole wheat flours that can impart sweetness and complex flavors. These grains can be easier for home bakers to handle and let us cast off the idea that whole wheat bread is the heavy and dense loaf we associate with ’70s-era hippie food.

These grains can be easier for home bakers to handle and let us cast off the idea that whole wheat bread is the heavy and dense loaf we associate with ‘70s-era hippie food.

Still, some bakers are trying to meet people where they are. The New York Times recently reported how a collective of 40 or so bakeries, connected to The Bread Lab, are having trouble selling whole wheat bread that doesn’t look like the squishy, pre-sliced, plastic-wrapped versions in the grocery store.

Jones founded The Bread Lab in 2011 and has since spearheaded grain research that led a nationwide resurgence of regional grains that taste good, have a high yield, and are better for you than commodity wheat. The goal is also to connect people to regional ingredients in a way that buying a bag of Pillsbury flour does not.

The bakeries — such as Mediterra Bakehouse in Pittsburgh, Elmore Mountain Bread in Vermont, and Lost Bread Co. in Philadelphia — have embraced a 100-percent whole wheat bread called “the approachable loaf” that looks like the bread in a bag you’d find in the store and is comparably priced. (Over at Community Grains, Klein is offering par-baked loaves online and in select California stores.)

Back at Oliveto, which is now carrying Boichik Bagels in addition to Community Grains breads, Winston and Klein noted the sweetness of a recent batch of whole wheat bagels.”The wheat brings in a whole lot of character,” Winston said.

Held up against the Manhattan-style bagels of her youth, “it’s not even trying to be the same thing,” she said. “You can really taste this whole wheat. I’m not trying to mute it — it’s just kind of being celebrated.”