Sourdough: The Science Behind a Pandemic Staple

Three Tufts experts share their research into microbes and fermented foods and offer new insight into sourdough’s distinct taste
Two loaves of crusty bread on parchment paper. Three Tufts experts share their research into microbes and fermented foods and offer new insight into sourdough’s distinct taste
“There are things people do in specific places that impact the crust, flavor, and other properties,” Benjamin Wolfe said. “Microbes play a big role, but it’s not just all about them.” Photo: Jessie Ellis
January 26, 2021


With the cold weather these days, one pandemic trend is continuing to warm people’s homes: sourdough baking.

The process of making a loaf with live fermented cultures has risen in popularity since last March—largely because the yeast shortage early in the COVID-19 pandemic took other breads off the table, and because many people are spending more time at home, according to Benjamin Wolfe, who studies microbial ecology and evolution in his lab at Tufts. (See "Nine Tips to Make Sourdough.")

“It’s really great during stressful times—it’s sort of like a creature, and you’re taking care of it. It’s a fun distraction, and if you get great bread, all the better,” said Wolfe, who recently published a paper on the varieties of microbes in sourdough starters in the journal eLife.

Liz Landis, a student in Wolfe’s lab and a first author on the eLife paper, agreed. “It’s such a careful endeavor and you really have to give it a lot of attention, which may be why it has experienced a lot of resurgence during COVID-19,” Landis said.

Jessica Ellis, N20, a researcher in the Vitamin K Lab at the Jean Mayer USDA Human Nutrition Research Center on Aging (HNRCA) at Tufts, said she used to make sourdough only on weekends, but expanded her baking hours during the pandemic.

“Once you start a loaf, there are several steps that only take a couple of minutes to do, but are spaced several hours apart,” said Ellis, who studies bacterially produced forms of vitamin K. “So now it’s more feasible to make sourdough during the week working from home.”

Benjamin Wolfe and Liz Landis in pre-COVID times with some of the starter samples they received in the mail for testing. Photo: Courtesy of Ben WolfeBut what exactly gives sourdough its distinct taste? How do microbes transform bread, and other fermented foods such as kombucha and sauerkraut that are seeing a boom during this time? When it comes to this pandemic staple, there’s a good deal of misunderstanding, according to Wolfe, Landis, and Ellis—and much more to appreciate.

“People have been making sourdough in North America for a long time,” Wolfe said. “It’s been really fascinating to see how much of a role it’s played in this very stressful time.”

The Fermentation Game

Although most people have heard of fermenting foods, there’s some hesitation about how to go about it safely.

“When I first started with fermentation, some of my roommates were scared to try it,” Ellis said. “But fermentation is one of the oldest methods of food preservation and transformation. A lot of foods include fermentation in their processing that people don’t realize—like coffee or chocolate.”

Bread doesn’t immediately come to mind as an object of fermentation, either—but it’s one of the more straightforward foodstuffs you can transform this way, according to Ellis. “Some require more intentional culturing, and others are more spontaneous,” she said. “If you leave milk out, it’s just going to spoil—it won’t turn into yogurt. But sourdough kind of works on its own.”

The process begins with a starter, or a small amount of flour and water. You let the mix sit for about 24 hours, then take a small part of it and mix it with fresh flour and water. This is repeated every day for two to three weeks, at which point the microbes are active enough to start the dough.

Sourdough is more forgiving of mistakes than some other fermented foods, which makes it ideal for beginners. “Sourdough starters are pretty resilient. If you forget to feed it, or add too much or too little flour or water, you can usually revive it without having to start over completely,” Ellis said.

It’s also more dramatic in its transformation. “It has both yeast and bacteria, which changes the texture of bread, makes it rise, and gives it a sour taste, which I think makes it fun,” she said.

A sourdough starter. “Fermentation is one of the oldest methods of food preservation and transformation,” said Jessie Ellis. Photo: Courtesy of Jessie EllisBut one popular claim about sourdough should be taken with a grain of salt, Ellis cautioned—the idea that it’s necessarily healthier than other breads. Some studies have shown that fermentation can reduce levels of short-chain carbohydrates that are difficult for the small intestine to absorb, which would make sourdough more tolerable to people with irritable bowel syndrome, Ellis acknowledged. But other studies have yielded conflicting results; plus, it’s unknown whether the reduction in these carbohydrates would be clinically significant, she said.

“There’s a lot of potential for fermented foods and a lot of enthusiasm around them, but in terms of the science for many of them, clinical trials are still pretty sparse,” Ellis said.

Ellis is now exploring the potential benefits of a nutrient present in many fermented foods: manaquinones, which are bacterially-produced forms of vitamin K.

This is significant because leafy greens were previously considered to be the main dietary source of this vitamin. In particular, Ellis has been looking into the effect of these vitamin K forms on the gut microbiota. “Measuring foods in the lab like this was what sparked my interest in making sourdough,” Ellis said. “It’s fun to play with your food.”

Edible Petri Dishes

While most breads require yeast, all you need for sourdough is flour and water. Microbes are already present in flour, and they begin to multiply when water is added.

“By mixing flour with water and constantly adding fresh flour, you’re waking up those dormant microbes,” Wolfe said. These self-contained collections of bacteria are ideal for a lab like Wolfe’s, which studies the cultures in fermented foods in hopes of better understanding the human microbiome.

“Essentially, they’re little edible petri dishes that people are putting out on their countertops, to create microbial ecosystems in their kitchens,” he said.

Sourdough starters are also ideal for study because people make them all over the world, Wolfe said. As microbial ecologists, his team is interested in how cultures vary from place to place. That’s what inspired their recent study published in eLife.

“The idea is that in Boston and New England, there may be unique microbes, yeast, and bacteria that you don’t necessarily find in Europe or San Francisco or South America, and that those distinct microbes could affect the flavor and quality of the sourdough,” Wolfe said. He pointed to San Francisco, whose sourdough has the reputation of being superior to other varieties.

“We wanted to get insight into what microbes were growing in people’s home fermentations, and determine how these different microbes impact the way it smells and how fast the dough rises,” Landis said. “It’s important for breadmakers, especially industrial breadmakers, to be able to refine their methods of sourdough making—but we were also more broadly interested in how microbiomes are shaped, and its implications for microbiologists.”

Wolfe and Landis took this question on in partnership with the University of Colorado at Boulder and North Carolina State University. In 2016, they began soliciting sourdough starters from a variety of places. Upwards of 500 starters came in the mail. “They kept coming and coming. We were bringing up these giant bins of packets that smelled a little funny,” Wolfe said. “People were starting to look at us strangely.”

Landis enjoyed smelling all the samples, and was inspired by people’s recipes, photos, and family breadmaking histories. “There’s already such a wealth of expertise here. It’s the oldest form of breadmaking, and it’s really lovely to think about the heritage and legacy of bakers from the past,” she said.

“Sourdough starters are pretty resilient. If you forget to feed it, or add too much or too little flour or water, you can usually revive it without having to start over completely,” Jessie Ellis said. Photo: Courtesy of Jessie Ellis“People are already managing microbial populations when they make their sourdough, even if they might not necessarily know what the names of the species are,” she added.

Wolfe and Landis worked with chemists at Tufts to analyze the microbes in the samples. “We found that one group of bacteria, the acetic acid bacteria, had a disproportionate role in shaping the properties of sourdough. It’s studied more in vinegar production and kombucha,” Landis said.

“Thirty percent of the starters we studied had this group of bacteria, and these starters had significantly different aromas coming off them, and tended to rise more slowly,” she added. “They found that the age of the starter and whether or not it was bought from a commercial source tended to affect which microbes were present.”

However, they also found that the microbes in sourdough starters didn’t vary from location to location—they were much the same in Boston as they are in San Francisco.

“There are things people do in specific places that impact the crust, flavor, and other properties. It could also be that San Francisco does a great job marketing its sourdough,” Wolfe said. “Microbes play a big role, but it’s not just all about them.”

Why are people willing to put in so much effort for a loaf of bread? It’s the same reason Wolfe has spent so much time studying these efforts. “At the end of the day, people love it,” Wolfe said. “With the current craze, it’s exciting to think about future directions, and where sourdough will go from here.”

Landis is honored to play a small role in that evolution. “I really love sourdough, and more than that I love sourdough bakers because they care about it so much,” Landis said. “It’s really a privilege to receive a piece of something so important to them, and to be able to give them more information.”

Nine Tips to Make Sourdough

Go online. Wolfe recommends Andrew Janjigian’s Instagram account, @wordloaf, while Ellis recommends the blog Perfect Loaf. “If people want to get very meticulous, it has a great step-by-step tutorial,” Ellis said.

Start small. “One thing people don’t like about sourdough is that you often use a lot of flour as you keep feeding and discarding it,” Wolfe said. “I have tried to play around with how small I can make a starter to reduce the overall amount of flour I’m using.” There’s even a hashtag for this type of micro-starter: #quarantiny.

Measure carefully. When making your own starter, it’s best to go not by volume of ingredients, but by weight. Ellis suggests using a kitchen scale to weigh ingredients.

Switch up your flour. “If your sourdough starter attempt doesn’t work the first time, try a different flour,” said Wolfe. “Different flour brands, even the same type of flour from a different company, will have different microbes.” Rye flour is minimally processed, which could lead to more and healthier microbes in your sample, Wolfe said.

Maintain multiple starters. “Over time, you might find yourself using one over the other, because you might prefer the characteristics of those microbes,” Landis said. “Yes, technique is important, but the biggest thing I’ve learned is that the starter you use really matters.”

Tweak your process. “There are so many different techniques people employ, like manipulating the temperature of the starter or changing the amount of time rising the dough to get different rises,” Landis said.

Get creative. Wolfe has experimented with adding some unlikely ingredients into his starters, such as a tablespoon or two of miso. “Miso is another fermented food with a complex microbial community, which can really boost the microbial profile of your starter,” Wolfe said. “It ends up tasting like burnt chocolate or soy sauce and adds an awesome complexity.”

Log your efforts. “People keep notebooks and log data about their sourdough breadmaking,” Landis said. “It reminds me of lab science, especially the way people share their protocols—it’s so specific.”

Branch out. If you want to further explore the fermented food world, kombucha is a great next step. Ellis said she and her classmates at the Friedman School used to pass around kombucha scobies, or disks of bacteria and yeast from previous batches that can be used to create new ones. “You combine it with sweet tea, add ginger to make it fizzier, and put a coffee filter with a rubber band over the top of the jar,” Ellis said. “It doesn’t take a lot, and it’s low maintenance—anyone can do it.”

Monica Jimenez can be reached at