The Science of Sourdough: A perfect love story of yeast and bacteria

The essence of the perfect slice of sourdough bread is in the air right now. It is even on your hands. The heart of the sourdough is the starter, a fermented culture of flour and water. The sour flavor of the dough comes from lactic acid bacteria (LAB) who live in relative harmony and competition with yeasts. The starter (also called “levain” or “mother”) is the source of all of the good qualities of sourdough bread: the tang, the spongy texture, and the nutritional properties.

Although yeasts are commonly associated with baking and other fermentations, the forgotten heroes are the LAB who generally outnumber yeasts by 100:1 in the starter1. The initial mixture of flour and water makes an excellent home for LAB with an initial pH of 5.0-6.2 – which is more acidic than water – and rich in carbohydrates for the bacteria to consume. In these favorable conditions, lactobacillus species, such as L. sanfanciscensis, flourish and outcompete other types of bacterias. Lactobacillus are used in the production of many fermented foods such as sauerkraut, beer, kimchi, and yogurt. They are also important participants in the body’s ecosystem and maintain the pH of the digestive and genital systems. The production of lactic acid by bacteria is actually the same reaction as the production of lactic acid in your muscles after hard exercise. This type of reaction is anaerobic, not facilitated by oxygen. In the case of muscles, energy is used faster than blood cells can provide oxygen so the muscle cells turn to anaerobic reactions to match their needs. For lactobacillus, the anaerobic pathway is their only option but they are still tolerant to exposure to oxygen. LAB is your companion through every meal and every trip to the bathroom, the friend you never knew you had. There are more than 50 species of LAB endemic to sourdoughs with more that have yet to be identified (). The first microbial residents of a new starter can be sourced from the air, naturally in the flour, and from the baker’s hands2.

Sourdough lactobacilli are able to colonize flour batters due to their specialized metabolism which digests maltose and fructose. Maltose and fructose are two sugars,the simplest forms of carbohydrates. These sugars are chemically simple and store lots of energy, making them excellent fuel for fermentation. As the LAB consumes sugars they produce both energy and several types of by-products. The three types of LAB present in the starter and their ratios control the flavor profile. Per sugar metabolized: homofermentative lactobacilli produce two lactic acid molecules; Heterofermentative lactobacilli produce one lactic acid and one either ethanol or acetic acid; finally facultatively heterofermentative lactobacilli can act as either type3. All types of LAB are present in sourdough starters. Acetic acid gives the bread a tangy, vinegary flavor while lactic acid imparts a creamy, yogurt-like taste. Controlling the production of acetic and lactic acid will control the flavor of the sourdough. For the most intense sourdough, heterofermentative and homofermentative activity are necessary. This can be affected by the temperature, flour used, and the hydration of the dough. Increasing the temperature and the wetness will increase most microbial activity, think of that container of milk left out in the sun. Under warmer, wetter conditions (approximately 90 °F/32 °C) the homofermentative and heterofermentative LAB will increase their production of lactic acid and facultatively heterofermentative which can choose either pathway will choose the easiest and produce lactic acid. This environment will result in not only a more flavorful bread but also a more nutritious bread as the acid increases the availability of nutrients4. Besides tasting the bread, a good way to estimate the acid composition of your starter is by smell: high lactic acid and it may smell like yogurt; while high acetic acid and it smells more like vinegar.

While many bacteria cannot survive in acidic conditions, lactobacilli have stress response mechanisms that allow them to live in low pH environments. Part of the success of the LAB is due to its ability to produce antimicrobial peptides, bacteriocins, that act as natural preservatives and inhibit the growth of pathogenic microbes such as listeria and staphylococcus. LAB produced bacteriocins are also being studied as antibiotics.

While the stage is set by the lactobacilli, yeast plays an equally important role in the leavening process. The starter is a biologic leavening agent, gas-producing agent, as opposed to baking powders. Enter Saccharomyces cerevisiae whose name literally means “sugar-mold” while cerevisiae comes from the Latin word for “beer”. The yeasts compete for sugars and metabolize them into ethanol and most importantly carbon dioxide. This carbon dioxide produces the characteristic bubbles of the starter which then translate after baking to lovely spongy bread. This is what also increases the volume of the starter sometimes in volcanic fashions (Picture of overflowed starter). Part of maintaining a healthy ecosystem in the sourdough starter is feeding it. It is alive after all. The microbes quickly eat available nutrients typically only 1-2% of the flour. An unfed starter will see decreasing productivity of LAB and yeast as they starve and might become breeding ground for molds.
The yeasts and the LAB (and other bacteria you don’t want) are always in an intricate sugary dance of resources. One remarkable such ecosystem exists between L. sanfranciscensis and candida milleri. L. sanfranciscensis acts as a heterofermentative bacteria which produces both lactic and acetic acid and it is unique because it prefers maltose sugars over glucose. When it metabolizes maltose and fructose, the most common sugars in flour, part of the reaction produces lactic and acetic acid while the other part of the reaction produces glucose. The increasing pH can be an issue for many microbes but not for C. milleri who is hungry for glucose and cannot metabolize maltose. Most LAB and yeast prefer glucose over other sugars and thus L. sanfranciscensis can protect its own food source, maltose.
The sourdough starter is a unique ecosystem we are just starting to understand in a scientific way but have depended on for thousands of years.

It illustrates that something as simple as good bread incorporates the fight for survival, partnership, and complex biochemistry. So next time you crunch into some tangy chewy bread, spread your butter on a baguette or enjoy a great sourdough BLT, take some time to thank the millions of microbes that made it happen.

Thanks, obligately heterofermentative lactobacillus.

Sourdough bread. Delicious. Credit:
Lactobacillus acidophilus (homofermentative) under a microscope with numbered ticks 11 μm apart. Credit: Bob Blayblock.

Overflowing sourdough starter indicates strong yeast activity. Credit:

Saccharomyces cerevisiae with a 5 μm scale bar. Credit: Mogana Das Murtey and Patchamuthu Ramasamy.

– By Allison Kubo


Ottogalli, G., Galli, A., & Foschino, R. (1996). Italian bakery products obtained with sour dough: characterization of the typical microflora.

Reese, A. T., Madden, A. A., Joossens, M., Lacaze, G., & Dunn, R. R. (2020). Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread. mSphere, 5(1).

De Vuyst, L., & Neysens, P. (2005). The sourdough microflora: biodiversity and metabolic interactions. Trends in Food Science & Technology, 16(1-3), 43-56.

Fretzdorff, B., & Brummer, J. M. (1992). Reduction of phytic acid during breadmaking of whole-meal breads. Cereal Chemistry, 69(3), 266-270.

Perez, R. H., Zendo, T., & Sonomoto, K. (2014, August). Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications. In Microbial cell factories (Vol. 13, No. 1, p. S3). BioMed Central.

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Lexie and Xavier, from Orlando, FL want to know:
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Even though it’s been a warm couple of months already, it’s officially summer. A delicious, science-filled way to beat the heat? Making homemade ice cream.

(We’ve since updated this article to include the science behind vegan ice cream. To learn more about ice cream science, check out The Science of Ice Cream, Redux)

Over at Physics@Home there’s an easy recipe for homemade ice cream. But what kind of milk should you use to make ice cream? And do you really need to chill the ice cream base before making it? Why do ice cream recipes always call for salt on ice?

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