#FEMSmicroBlog: Unravelling the secrets of sourdough


Scientists from across Europe are working together to find interesting microbes in sourdough starters. Vilhelmiina Haavisto explains for the #FEMSmicroBlog the successes and challenges of such an intensely collaborative project. Keep reading to find out how you can contribute to this project and become a citizen scientist! #TheCulturePlate


Investigating the microbiome of sourdough

Fermented foods, like kimchi, cheese, and pickles, are staples in many cultures across the world. One well-liked fermented food is sourdough bread, which is made from a starter culture. Keeping sourdough starters is especially popular in Europe and North America, and gained many hobbyists early in the COVID-19 pandemic. To maintain a starter, hobbyists need to regularly add flour and water to trigger the fermentation process, a process often called ‘feeding your starter’.

A sourdough starter contains living microbial communities consisting of yeasts and bacteria, mostly from the orders Saccharomycetales and Lactobacillales/Rhodospirillales, respectively. These microbes leaven the dough by producing CO2 and produce molecules and enzymes that impact the texture, flavour, and even nutritional profile of the baked bread. For example, some of the Lactobacillales produce lactic acid, which contributes to the characteristically sour taste.

Yeast (left) and lactic acid bacteria (right) isolated from sourdough.
Yeast (left) and lactic acid bacteria (right) isolated from sourdough. Credit: Annina Meyer


Annina Meyer and Jan Tan, two doctoral students at ETH Zürich in Switzerland, are collecting and characterising the microbes of sourdough starters in close collaboration with several research institutions across Europe. Their project is part of an international consortium called HealthFerm, whose aim is to better understand the microbial players in the fermentation process and how they impact foods and our health.

“We want to collect and characterise as many microorganisms as possible from sourdough, and choose the best ones for biotechnological applications”, Meyer explains. “It’s about having a resource to help redesign fermentation.”

Colonies of lactic acid bacteria turn blue due to acid production, colonies of yeasts remain white.
Colonies of lactic acid bacteria turn blue due to acid production; colonies of yeasts remain white.


HealthFerm includes project partners from 11 countries across Europe, including universities, research institutes, and private companies. Their ultimate goal is to develop novel fermented foods and improve existing ones. Although fermented foods are already hailed as ‘superfoods’, improving their nutritional profiles and the efficiency of the process could promote healthier and more sustainable diets in the future.


Sampling sourdoughs across Europe with the help of citizen scientists

A key aspect of the project involves the citizens who generously donate samples of their sourdough starters. “The citizen scientists are so motivated…and like to interact”, Meyer says. Anyone can participate – the team has received samples from sourdough enthusiasts, bakeries, their colleagues, and even a sourdough pizza restaurant in Zürich. Participants receive a sampling kit which they send back with their sourdough starter samples inside.

When a sample arrives at the lab at ETH Zürich, it is processed immediately. “Our days can be unpredictable,” Tan says, “since sample [processing] can be quiet one day, and very busy the next.” The team is frequently surprised by the different appearances and smells they encounter, and the starters can look stunning under a light microscope.

Sourdough under a light microscope at 400x magnification. Credit: Annina Meyer
Sourdough under a light microscope at 400x magnification. Credit: Annina Meyer


These glimpses “illustrate just the tip of the iceberg of biodiversity which we expect to unravel within these hundreds of collected sourdoughs”, Meyer enthuses. Some measurements are done straight away, but others, to determine in detail which microbes are present and what they are doing, must wait until enough samples have been collected.


The future of fermentation relies on citizen scientists

Meyer and Tan have already collected around 200 samples, but recruiting citizen scientists is no easy task. “It requires a lot of effort to get samples,” Meyer says. “We haven’t yet cracked the code,” Tan adds. The multicultural and -lingual nature of Europe presents a challenge for advertising, and Meyer, Tan, and their collaborators are still actively looking for participants across Europe. Sometimes, they strike gold – for example, after a German sourdough blogger promoted the project, they received around 80 new registrations, and an article in the Swiss newspaper 20 Minuten brought in over 150 new registrations.

After the entire consortium has collected enough samples, Meyer and Tan will begin the in-depth analysis of the samples they have received. This will involve a multi-omic investigation to thoroughly characterise the starters and find microbes with interesting traits. So far, food microbiome studies have never included such an in-depth multi-omics investigation, nor has anyone aimed to build such an extensive collection of microbes for use in food biotechnology.

All samples, individually isolated microbes, and sample metadata will be integrated into an ‘Open Food Microbiome Atlas’, providing a resource for future steps in the HealthFerm project, such as designing engineered fermentation. “This large collection opens up many new project directions, and provides a good base,” Meyer explains. “The interesting stuff is yet to come,” Tan adds.


About the author of this blog

Vilhelmiina Haavisto is a freelance science writer and PhD student at ETH Zürich in Switzerland, where she studies marine microbial communities.



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