The flour you choose helps decide which microbes run your sourdough and how it tastes.
Sourdough starter is made from just flour and water, yet it supports a complex process that bakers rely on every day. Beyond baking, it also offers scientists a unique window into how microorganisms interact and evolve. The familiar chewiness and tangy flavor of sourdough come from microbes that ferment the dough. Previous research has identified more than 60 different bacterial genera and over 80 yeast species in sourdough starters collected worldwide. “We can use sourdough as an experimental evolution framework, to see what happens over time,” said evolutionary biologist Caiti Heil, Ph.D.
How Flour Type Shapes Sourdough Microbes
In a recent study published in Microbiology Spectrum, Heil and her colleagues at North Carolina State University in Raleigh examined how different flours influence the microbes that grow in sourdough starters. Their analysis showed that yeasts belonging to the genus Kazachstania were the most common in every starter they tested. In contrast, the bacterial communities differed depending on which type of flour was used.
Why Flour Choice Matters for Bakers
The results suggest that switching flours can change the microbial balance of a starter. “And because the microbial composition affects different traits, by altering the flour you could potentially alter how your bread tastes,” said Heil, the senior author of the study. More broadly, she explained that the findings demonstrate how sensitive the sourdough microbiome is to environmental factors.
Many Influences on the Sourdough Microbiome
Earlier studies have shown that sourdough microbes are shaped by several factors. These include the ingredients used, the surrounding air and kitchen surfaces, and even the hands of the baker. Bakers also work with a wide range of grains, such as wheat, rye, barley, teff, and millet. Each grain provides a different set of nutrients that microbes use to grow and compete.
A Classroom Project Sparks Scientific Research
The study began with an educational project led by Enrique Schwarzkopf, Ph.D., a postdoctoral researcher in Heil’s lab and an avid sourdough baker. He launched a program at a local middle school to teach students about fermentation and evolution. Schwarzkopf, who maintains a sourdough starter named Seth, used the starter as a hands-on teaching tool. Students experimented with different flour combinations and feeding schedules to see which starter would grow the fastest.
Tracking Microbes With Genetic Tools
To study the starters, Heil and her team used metabarcoding, a technique that scans genetic material to identify which microbes are present. Each starter began with one of three substrates: all-purpose flour, bread flour, or whole wheat flour. At the start of the experiment, the flours contained similar bacterial communities along with a variety of yeasts.
Unexpected Results From Fermentation
After several weeks of repeated feeding, the microbial communities changed. The starters all became dominated by the same yeast, while the bacteria showed greater variation. Heil said she initially expected to find Saccharomyces cerevisiae, or brewer’s yeast, which is commonly used in baking and is central to many of her lab’s research projects.
Instead, Kazachstania emerged as the most abundant yeast in every starter, regardless of flour type or feeding schedule. Genetic analysis also revealed differences among bacteria. Starters made with whole wheat flour contained higher levels of Companilactobacillus, while starters made with bread flour showed increased levels of Levilactobacillus.
Flour as an Ecological Driver
Heil, whose research focuses on how organisms adapt to new environments and compete at the genetic level, explained that each flour type creates different nutritional conditions. Linking those substrates to the environments microbes experience, she said, can help scientists better understand how diverse microbial communities form, compete, and persist.
Reference: “The role of flour type and feeding schedule on the sourdough microbiome” by Sima Taheri, Enrique Schwarzkopf, Hanna L. Berman, Nathan Brandt, Jessica McNeill, Nico Sevier, Margot Ruffieux, Robert R. Dunn and Caiti Smukowski Heil, 25 November 2025, Microbiology Spectrum.
DOI: 10.1128/spectrum.02380-25
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4 Comments
So, where is the recipe?
Thanks Kelly, for sharing your observation. I loved the article and reading your comment was a bonus!!
Hello, I found this article very interesting, especially the comment about how different microbial makeups on the actual hands of the bakers can make a difference. I have noticed every season, as I sell my sourdough at local farmers markets, that at the beginning of the season when all my new hires begin, that my breads don’t rise nearly as well. I stand shoulder to shoulder with these new hires, taking them through the recipe step by step, giving them knowledge so that they understand what they are doing during the process, as well as education on the process itself. So the recipes are followed, the fermentation schedule is followed, the methodology is the same. And the breads do not turn out as well, why??? This is been observed through several seasons. Near the end of our season, which runs from May until the end of October, finally the bread start to come around again. We are obviously influenced by season and temperature. Although the bakery is half below grade so remains cooler than outside temperatures, and thus reasonably constant all year. And when all my staff leave for the season, the bread becomes its most glorious of the year.
I did meet someone at one of my markets this year, with a Ukrainian grandmother, who used to tell her not to bake bread while she was in a bad mood because the bread responds to our moods. Make of that what you will!
What about those of us who are celiac ? Does the flour change to gf flour using the sourdough starter?