The Science of Sourdough

In this Zoom Forum, Bob Holmes, a science writer for Knowable Magazine, brought together Guylaine Lacaze, the head of sourdough research at Puratos, a baking consulting company, and Karl De Smedt, curator of the Sourdough Library at Puratos, and Dr. Erin McKenney, a microbial ecologist at North Carolina State University, to discuss the unique organic chemistry and microbiology surrounding sourdough starters.

Holmes, the host, opened by saying what we all know: 

“One way that many of us have been coping with the coronavirus pandemic is by baking. And sourdough bread has been a big part of that. You’ve probably noticed it on social media all over the world. People are posting photos of their sourdough bread and the starters that leaven those loaves”

Holmes explained, “Starters are very interesting in their own right because they’re actually very complicated complex microbial ecosystems that scientists are really just beginning to understand.” Then he invited Dr. McKenney, who came with just one sample starter that she had named “David Doughy,” to comment.

“I’m down to just one these days, but at some point, I think I had 24 starters, but it was a bit much,” she demurred. Then she explained what was in this start, “We have these relatively complex communities of many different types of yeast, as well as, lactic acid-producing bacteria and acetic acid bacteria.”

Then the host asked Lacaze, “Could you tell us a bit more about that and what you found. Where did those microbes come from?”

She responded: “In our study, we wanted to know if once a microflora is established in a dough, would it be possible to change it by using another flour other than the one used to refresh it.” However, she added, when a starter is active and stable you can change the flour, but “it will not have a lot of impact on your flora.”

Both Lacaze and De Smedt were seated in the Puratos Sourdough Library, which made for an interesting backdrop. This repository of natural ferments from around the world has come from 130 sources, but their team of researchers have identified more than 1100 different strains of microorganisms in just those starters.

“But even if every sourdough is different, might they fall into several distinct groups based on the microbes that are present, in much the same way that terrestrial plant communities can be grouped into grasslands and forests despite a changing mix of species? The answer to that question might be coming soon. Elizabeth Landis, a microbiologist at Tufts University in Boston, and her colleagues (including Madden and McKenney) identified the microbes in 560 starters submitted by bakers around the world, then looked for recurrent groupings of microbes. Some species do appear to co-occur frequently, they found, perhaps because they specialize in feeding on distinct sugars… which is therefore available for the lactic acid bacteria.”—Bob Holmes, Knowable Magazine, August 13, 2020

I was personally excited to learn that anyone can register their own sourdough starts with them online. I registered my Riverside Lodge COVID 2020 starter this week. (Just go to questforsourdough.com to register yours too.) And this of course, all points generally to the fact that “no two sourdoughs are the same,” De Smedt clarified.

Pointing to the library, he said, “All these starters are unique. Some may look the same but there is a different combination, or a different consortium, of microorganisms in each. Some have similar flavor profiles but still, they all are different. So, yes I would say, and I think that Erin and Guylaine can confirm that, every sourdough is unique.

To test this, a few years back Puratos, selected five distinct starters but used them to bake five different tasting breads using the same flour and baking process. They saw some interesting, but nice differences in the flavor profile,  texture, and also in the fermentation power—”some do have more fermentation power than others. So yes, we could say that every starter is unique,” he concluded.

Starters all begin with flour and water. But then the baker’s microbiome and his or her environment contribute something, as does the flour itself. In fact, Dr. McKenney explained what really begins just as a “glorified papier-mâché paste” of just flour and water, transforms into a colony of bubbling, doubling, leavening, in a unique community of living organisms. She explained, that in the colonization process of the flour, there are standard stages of succession before it becomes a viable enough to bake with.

She learned this last summer, first hand when she partnered with four middle school teachers in Raleigh, North Carolina and one undergraduate researcher from Florida. Together they grew 40 starters from ten different types of flour, four starters from each kind of flour to the steps of succession. Together thay asked, “How does a sourdough starter grow up? And does that process change depending on the type of flour that you’re actually growing that starter from?”

The freshly milled grains were taken from a local business to ensure maximum enzyme activity in the flour. Then they sequenced the DNA from just the flour and just the water in the starters after one day, two, three, six, ten, and fourteen. They also took pH measurements watching it drop “precipitously in the first three days, then measuring the height of it over time to see how it increases.”

Carefully measuring the pH of lactic acid and acetic acid producing bacteria helped them conclude, “The more acid that you have, the lower your pH is going to go.  And the higher your sourdough starter is rising in the jar, that’s indicative of healthy, prospering yeast communities that are producing a lot of carbon dioxide.”

Studying both DNA and pH, they “were able to identify days one, two, three, six, ten, and fourteen, which is really interesting as we try to figure out what microbes are in there—the bacterial communities were changing very dynamically.

“At day one the starter looks essentially the same as the flour inputs. Initially, flour plays a very heavy role. Or there are also environmental inputs, possibly from the mill where the flour was ground. Whatever microbes are in the flour tend to be present at very high relative abundance on day one.

“I’ve been studying microbes in labs for over a decade and now I’m completely humbled by sourdough; I learned to trust the microbes. Because from day three to about day six you see this shift in the community toward bacteria that are completely acid-resistant because they are also acid producers. You also see a shift toward yeast that is also acid tolerant. …microbes have been on this planet way longer than we have they know what they’re doing generally trust the microbes

Dr. Erin McKenney

“But even as soon as day two, we start to see a shift toward acid-producing bacteria affiliated with the grain and with our bodies.” At first, just about any microbe can grow on this rich, new energy source, including spoilage bacteria. (That’s why brand-new sourdough starters often go through a black, putrid-smelling phase.)

“But soon, conditions begin to change. One group of those early colonists begins to acidify the starter. By Day 3, these so-called lactic acid bacteria — named for one of the main acids they produce, which is also found in yogurt, cheese, and other fermented milk products — have made the starter so acidic that many of the early colonists can’t survive, leaving only the lactic acid bacteria and a few acid-tolerant yeasts. This lactic acid, together with vinegary-smelling acetic acid, gives sourdough its characteristic tang.”

Lacaze stated that her research also shows that fermented bread cultures “may also improve the nutritional quality of the bread. The increased acidity activates an enzyme, phytase, that makes minerals like calcium and phosphate more available.”

Continuing, she explained, two weeks into a new starter’s life, it begins to settle “into a stable state where yeasts and lactic acid bacteria grow vigorously, the yeasts producing enough carbon dioxide to leaven a loaf of bread,” which make the starter ready to use in baking.

“But the fact that new starters settle down within a couple of weeks doesn’t mean that they all end up with the same set of microbes,” as the panelists pointed out early on. For example, Holmes reported that Lacaze and her colleagues tested this when they “shipped bags of the same flour to 18 professional bakers around the world, who then used the flour to create starters in their own kitchens using identical techniques. About a month later, the bakers and their starters convened in Belgium, where researchers used DNA sequencing to identify the microbes in each starter.

“Even though all the bakers started with the same flour, their starters were all different. Most contained various strains of common baker’s yeast, Saccharomyces cerevisiae, along with a host of other yeasts in varying proportions, they found. The starters also contained a wide range of lactic acid bacteria, mostly in the genus Lactobacillus—though once again, the details varied widely from one starter to the next. Most microbes appeared to have come from the flour—a different draw each time­—though a few also originated with the baker’s hands or kitchen.”

CARE AND FEEDING
Each microbial community seems to produce its own unique flavor profile, too, McKenney says. Some produce more lactic acid, which gives a yogurty flavor; others yield a sharper, more vinegary note from lots of acetic acid. And because each species of microbe has slightly different metabolic pathways, each is likely to add other flavorful metabolic byproducts to the mix — a big reason sourdough tends to have a subtler, more complex flavor than ordinary bread. “You could compare it to one single flower compared to a nice bouquet of different flowers. The complexity of all these different compounds is what you find in a sourdough bread,” says Karl De Smedt, who maintains a library of sourdough starters at Puratos.

Not everyone agrees that sourdough microbial communities are so variable. In commercial bakers’ sourdoughs, which are fed daily or even more often, the microbes always have plenty of food. That creates a race, with the fastest-reproducing microbes dominating over time, says Michael Gänzle, a food microbiologist at the University of Alberta, Canada. In the long run, he says, the winners are the yeast Kazachstania and the lactic acid bacterium Lactobacillus sanfranciscensis (recently renamed Fructilactobacillus sanfranciscensis).

That’s not necessarily good news for the resulting bread: L. sanfranciscensis grows fastest because it has one of the smallest genomes among lactic acid bacteria, which means it has fewer metabolic pathways and thus fewer flavor-producing by-products than other bacteria, Gänzle says. (Score one for home sourdoughs, which Landis says might be more diverse.)

But the flavor of sourdough bread depends on more than just the species of microbes present in the starter. “You can have really different sourdoughs even if the microflora is the same,” says Lacaze. “It depends also on the recipe of the sourdough, the parameters of the culture.” Stiffer starters — that is, those made with a lower proportion of water — trap more oxygen within the dough, and this encourages lactic acid bacteria to produce sharper-tasting acetic acid; in runnier starters, the same bacteria produce softer-tasting lactic acid.

Temperature matters, too. Lactic acid bacteria do best in relatively warm conditions, for example, so fermenting in a warm kitchen makes for a sourer dough, while cooler conditions lead to more of the fruity flavors produced by the yeast. Moreover, lactic acid bacteria, despite what you’d think, aren’t fond of highly acid environments. Home bakers who leave an acidic starter in a cold fridge for weeks between bakings can find they end up with a blander bread that lacks the distinctive tang contributed by the bacteria. (Pro tip: If you’re going to leave your starter in the fridge for longer than a week, make sure to refrigerate it immediately after adding fresh flour, when it’s least acidic. That, says Lacaze, will help the lactic acid bacteria survive the prolonged cold to acidify the rising dough.)

One of the biggest ways that bakers can influence the flavor of their sourdough bread is through their choice of flours for the starter. To demonstrate this, McKenney and her team made four starters each from 10 different grains. Because grains differ in the mix of sugars they make available to sourdough microbes — corn, for example, lacks a starch-digesting enzyme that creates maltose — they might lead to different sets of microbes and, hence, different flavors. And that’s exactly what McKenney found (again, the results are not yet published). Starters made from amaranth flour tended toward meaty, toasty aromas. Those made from teff (an African grain) and sorghum gave fermented smells, while emmer and buckwheat gave more vinegary starters.

So far, McKenney and other sourdough researchers have taken only baby steps toward designer sourdoughs: Their science has not yet caught up to folk wisdom. “People would like to know step by step: ‘How do I make the end product I desire?’” McKenney says. “We can’t begin to offer anything that’s better than common baking knowledge or the best practices you learn from blogs or talking to friends.”

More answers could be coming soon, thanks to new citizen-science initiatives. McKenney, Madden, and their colleagues run the Wild Sourdough Project, which invites home bakers to experiment with flours and growing conditions and report their results. Similarly, Puratos has launched the Quest for Sourdough, where anyone from newbies to professionals can register their sourdough. Those with particularly interesting or unique starters might be invited to submit them to Puratos’s sourdough library for further analysis.

But sourdough is interesting to more than just bakers. Sourdough and other food fermentations such as those that give us cheese, sauerkraut, and kimchi provide relatively simple, easy-to-handle model ecosystems for studying microbial ecology more generally. “There are lots of insights you can gain from studying fermented foods that you can then transfer to more complex microbial communities as well,” says Paul Cotter, a microbiologist at the Teagasc Food Research Centre in Ireland, and co-author of an article on food microbiology in the Annual Review of Food Science and Technology.

Sourdough offers an additional benefit, especially relevant in pandemic times when the microbial world seems so full of threat. “Sourdough is this one space where we all agree, as a society, that microbes are helping us do wonderful things,” Madden says. “If you love sourdough, you love wild microbes in our lives.”

This article originally appeared in Knowable Magazine, an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter.

*Editor’s Note (8/13/20): Our partners at Knowable Magazine have edited this sentence after posting to correct the described authorship of the study. Anne Madden and her colleagues conducted the study, not Erin McKenney and her colleagues, as was originally stated.