More Than Bread: Sourdough As a Window Into The Microbiome

Marcus Woo wrote . . . . . .

Benjamin Wolfe sticks his nose into a Ziploc bag and takes a whiff. “Ooh! That’s actually kind of nice,” he says. Inside the bag is a pungent, beige goop. It’s a sourdough starter — a slurry of water, flour, yeasts and bacteria — from which loaves of delicious bread are born. And it’s those microbes that have the attention of Wolfe, a microbiologist at Tufts University.

As the microbes munch on the sugars in the flour, they produce carbon dioxide, ethanol, acids and a smorgasbord of other compounds that give sourdough its bouquet of flavors and aromas.

It’s got “a little bit of buttery and barnyard,” he says. He hands me the bag to sniff, and surprisingly, it does smell like butter. But barnyard? “It’s like fermented hay and manure,” he explains. “But in a good way.”

This starter, which came in the mail from New York, and other samples sent by home bakers will be used to better understand how the mix of microbes in a starter imbues it with its unique flavor and character. The submissions are part of the sourdough project, a citizen-science initiative led by biologist Rob Dunn at North Carolina State University. Wolfe is a collaborator.

The project is trying to answer many questions: How does a starter’s microbial ecosystem vary with different flours? How does a new starter compare with one that’s 200 years old, filled with tradition and lore? Do they change with geography, as some claim? And, of course, how can you bake a more delicious loaf?

Not long after the researchers asked for volunteers last fall, I sealed my own starter in Ziploc bags and mailed it to Wolfe’s lab. About 1,000 others responded to the initial call, and 571 of them submitted samples — mostly from the U.S. and Europe, but also a few from Australia, New Zealand and even one from Thailand.

“In terms of getting a great depth of sampling across a huge geographic area, this is impressive,” Wolfe says. “We’ve never done anything like this for any fermented food before.”

The researchers are just starting to analyze the samples, but Wolfe hypothesizes that microbial variations will be determined more by whatever microbes are already in the flour than by geography. And a rough, preliminary analysis of a few samples seems to support that. Comparing East and West Coast starters hasn’t revealed any obvious differences so far. Another test shows that the microbes in different starters bought from King Arthur, a flour company, appear to be similar to one another.

For Wolfe, food is an avenue for his larger goal of trying to better understand microbial ecosystems, or microbiomes, which are found everywhere, from your gut to the oceans. In recent years, scientists have learned that microbiomes have an outsize influence on nearly every aspect of the world, including health, agriculture and the environment. Imbalances in our gut microbiomes, for example, have been linked to a laundry list of health issues, including obesity, colon cancer and autism. Last year, then-President Barack Obama launched the National Microbiome Initiative, a half-billion-dollar plan to study the microbiome.

Unlike most microbiomes, which contain up to thousands of species, fermented foods like sourdough, sauerkraut and kimchi have only a few to a couple of dozen species, making them easier to study. At the same time, they share commonalities with more complex microbiomes. For example, the microbiome on cheese rinds is similar to that on your skin.

Fermented foods, then, are like the lab mice of microbiomes, Wolfe says. “Just like how people can take a mouse and learn human biology, we’re taking fermented foods and trying to learn about microbiomes.” He wants to understand what environmental factors and biochemical processes determine which organisms can thrive in different microbiomes. The ultimate goal is to pinpoint the intricate molecular machinery that dictates how microbes interact and change over time under different circumstances.

And this kind of change can happen fast — within a few weeks, as Wolfe has discovered with his experiments on cheese. For example, a mold found on Camembert cheese called Penicillium (related to other molds that produce the antibiotic penicillin) grows blue-green and fuzzy in more austere, wild environments. “It looks like the thing that might rot your bread or fruit at home,” Wolfe says. It produces pigments and toxins that help fight off other microbes — a reaction to stressful environments.

But in the comfy confined environment of a cheese cave, for example, the microbe no longer needs those harsh survival tactics. It stops making toxins, loses pigment and takes on the familiar white of Camembert. “We can see microbes completely transforming their physiology in the cheese-making environment, which is really cool,” he says.

These changes aren’t necessarily new species but are akin to wine-grape varieties or dog breeds. They’re variations that give rise to the range of textures, aromas and flavors of cheese. Wolfe has been working with Jasper Hill Farm, a cheese-maker in Vermont, helping it to analyze its cheese microbes and better control flavors.

Wolfe and his colleagues are also studying salami, fermented cabbages like sauerkraut and kimchi, and fermented teas known as kombucha. Sourdough is just the latest to join the lab.

Back in the lab, Elizabeth Landis, a graduate student, is processing the new starter sample. After sterilizing a corner of the Ziploc bag with ethanol, she snips it with a scissors and squeezes some of the starter into small vials for freezing.

The frozen samples will be sent to Dunn’s lab to have their DNA sequenced to identify every single species in the starter. But to learn how microbes interact and evolve, Wolfe and Landis need their microbes alive.

So they freeze another sample with glycerol, which keeps the microbes viable. They will isolate individual microbial species, letting them grow on petri dishes under different conditions, like varying amounts of food and nutrients. Then, they can observe how the microbes react to and change in different environments.

Wolfe and Landis look at another sourdough starter under a microscope — the sample I had sent in a few months ago. I was curious: Was an imbalanced microbiome the reason my bread didn’t rise the way I wanted it to?

“You’ve got some good stuff!” Wolfe says. Right away, he spots a few globules and a bunch of smaller, pill-shape critters: yeasts and bacteria, respectively. The proper ratio of yeast cells to bacterial cells, he tells me, is about 1 to 100. “It’s a typical sourdough,” he says.

So it wasn’t my starter that was at fault, after all. It was me.

These samples will now go to Dunn’s lab, which is trying to take a DNA snapshot and capture the most detailed census ever of a sourdough microbiome. The researchers plan to begin sequencing the first batch of starters in a few months. The hope is that identifying individual microbes in the starters will help answer the hows and whys behind the spectrum of aromas and flavors in sourdough. What they learn may even help bakers create new kinds of even more delicious bread.

We may never look at sourdough the same way again. “We have these things right on our dinner plates,” Wolfe says. “Yet there are all these mysteries of the microbiome that’s right there that we haven’t figured out.”

Source: npr

The “No-Knead Bread” Chef Now Has the Secret to Sourdough

Kate Krader wrote . . . . . .

How do you explain America’s ever increasing obsession with bread, even as the ranks of gluten-free adherents continue to expand?

Credit one pioneer in the world of artisanal bread: Jim Lahey. At his Sullivan Street Bakery, which began in a tiny storefront in Soho in New York in 1994, Lahey baked monumental loaves such as the long, oval, pane pugliese with a sturdy, almost-burnt crust and chewy, moist interior. Soon, he was supplying bread to prestige restaurants around the city, including Jean-Georges and the Spotted Pig, as well as to upscale markets like Dean & Deluca.

Since then, Lahey has embarked on a mission to empower home cooks to bake their own bread. Through the University of Bread seminars he teaches at his bakery headquarters in New York’s Hells Kitchen, the “no-knead” method he introduced more than a decade ago has become a sensation, turning an army of hobbyists into passionate bread makers. No-knead bread, as the saying suggests, is a loaf made with minimal ingredients and work; the only thing you need a lot of is time—at least 24 hours.

But Lahey’s no-knead bread has become a victim of its own success. “Everyone is an expert now; no one wants to take those no-knead classes,” he told me, referring to “They want to learn the next thing.”

That new thing? Sourdough bread, with its yeasty, lightly tangy flavor and buoyant crumb. If no-knead is the beginner loaf for home bread bakers, sourdough is firmly in the intermediate category. No-knead bread is made with pre-packaged bakers yeast, a fast fermentation that works fine, according to Lahey in his forthcoming The Sullivan Street Bakery Cookbook (W. W. Norton & Co., November 2017). “But it tends to preclude the development of more interesting flavor.”

Lacey continues: “If you are like me and want breads that are not merely predictable but awe-inspiring—with an open crumb and a bouquet of unbelievable flavors—then you’re going to need a different kind of fermentation, one that relies on a sourdough starter.” He prefers a liquid-y starter style mixture that he calls a ‘biga’ to help the dough ferment and rise.

In his upcoming book, Lahey devotes plenty of room to topics like “a beautiful fermentation,” and he counsels readers on how to make their own. (His secret ingredient is a kale leaf, which has natural yeast clinging to it.) It’s a three-day process at minimum and can often take up to five days just to get the starter started, plus a couple of additional days to let it refresh.

For those who like short cuts, though, there is good news: Excellent ready-made starters are out there. The venerable baking company King Arthur sells a very good one, and Sullivan Street expects to have its own commercial product by this summer. Your local bakery or passionate bread baking neighbor might also be persuaded to give you starter for your bread.

In this exclusive preview, here is Lahey’s sourdough bread recipe, adapted from the The Sullivan Street Bakery Cookbook, co-written with Maya Joseph. It takes four steps and, with a starter, can be done in about four hours.


The Ultimate Fast Sourdough

“Often I counsel patience when baking—so very often, the only secret to making a good bread better is to wait a bit longer, and let the flavors, fermentation, and rise develop, “writes Lahey in the book. “But as an impatient guy, and there are sometimes when I want to mix, bake, and eat a loaf not tomorrow, but today. Here is a recipe for those moments. It’s not instant bread, but it is faster bread. ”

Yield: One 9-inch round loaf.

Equipment: A 4½- to 5½-quart heavy pot with lid; a large piece of parchment paper.

Ingredients:

100 grams prepared starter (such as King Arthur Classic Fresh Sourdough Starter)
200 grams (about 1 1/4 cups, plus 2 tablespoons) unbleached all-purpose flour
100 grams (about 2/3 cup) whole wheat flour
6 grams (about 1 teaspoon) fine sea salt
230 grams (about 1 cup, plus 1 tablespoon) 65ºF-70ºF water
Wheat bran, for dusting

Method:

1. In a large bowl, combine the white flour, wheat flour, and salt and whisk to combine. In a small bowl, whisk the starter and water until the starter is fully dissolved. Pour the starter mixture into the flour, and use a flexible spatula to quickly mix. Cover the bowl loosely with a clean kitchen towel, and let the dough sit at room temperature for 30 minutes.

2. Turn the dough, pulling it off the sides of the bowl and folding into the center as you turn; work it as little as possible. Cover loosely and let rest for 30 minutes before turning the dough again. After approximately 5 turns, or 2 ½ to 3 hours, the dough should be ready. (Don’t expect to see a big increase in size in this dough—by turning the dough every half-hour, you are doing what I call the lazy man’s version of kneading the dough—improving the texture without much effort.)

Note: How do you tell when it’s ready? You want it to get to the point where it is capable of holding a shape, and not ooze into a pancake when you shape it into a ball. It should be so interested in sticking to itself that it easily peels off the bowl when ready to shape.

3. Place a large piece of parchment paper on a sheet pan and cover with wheat bran, so that you can no longer see the paper. Transfer the dough to a lightly floured surface and form it loosely into a ball: hold it with both hands and gently tug the sides down and under, into the middle of the dough, to make a taut ball; don’t let the dough tear. Set the dough seam side down on the bran-coated paper. Dust the top of the dough lightly with more bran. Cover loosely with the towel and let it sit at room temperature until doubled in size, about 2 hours.

4. Preheat the oven to 500ºF (450ºF if your oven runs hot). Preheat a cast-iron ovenproof pot with tight-fitting lid, such as Le Creuset, in the oven. Carefully remove the lid and transfer the dough on the parchment into the pot. Use a serrated knife to score the loaf with a long slash, to allow the dough to expand. Cover the pot immediately and place the pot in the oven.

5. Bake the bread for 35 to 40 minutes with the lid on. Carefully remove the lid and tear off any excess parchment. Bake for another 10 to 15 minutes with the lid off, until the crust is a very, very dark brown. (I urge you to let the bread cook, uncovered, until the top of the bread nearly blackens and the sides reach a very, very, very dark brown.) Remove the loaf from the pot. Cool the loaf on a wire rack. The loaf will continue to cook as it cools, so try to wait an hour or so before cutting into it.

Source: Bloomberg