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Sourdough Microbiomes and Bread Flavor

Like many sourdough bakers, I’m intrigued by the debate about what determines a sourdough starter’s microbial composition. Is it the food source, the environment or terroir, storage temperature, frequency of feeding, baker’s hands, or all of the above? And once a starter is established, does a starter’s microbiome shift if you change any of these factors? And do any of these microbial goings on affect the appearance or flavor of bread baked with them?

Bakers tend to agree that starter hydration and storage temperature can encourage some microbes to flourish over others; e.g. the use of low hydration pasta madre to make heavily enriched panettone. It’s also commonly accepted that whole grain flour will make a starter’s microbes multiply faster than refined flour. But debate continues about whether an established starter changes if moved to a new location or if fed a new flour or wheat variety.

I recently learned more about the work of the Puratos World Heritage Sourdough Library in Belgium. This library houses over 130 sourdoughs from more than 23 countries, and refreshes the starters with their original flours, using the original methods. (The storage temperatures may differ from the original customs.) In 2018, the sourdough library did a research study which demonstrated that sourdough starters remained unique even when fed identical flour for a short period of time. In the study, 15 bakers were sent new flour to use for 10 feedings. The 15 bakers then traveled to the library and baked breads with their starters. The bakers detected different flavors in the breads despite the period of identical feedings.

Learning about this research and also reading the research of @benito into rye starter pH and buffering ability in this forum thread inspired me to do this experiment where I created a new sourdough starter from rye flour and compared it to an all purpose (AP) sourdough starter that I converted to rye flour. I wanted to see if the starters would behave the same because they were created in the same kitchen and now being fed the same flour, or if the biomes would be different and persist in being different over time.

Pain de campagne using bread flour, home-milled rouge de bordeaux wheat, and two different home-milled rye flour sourdough starters. Baked six weeks into the experiment, these loaves look similar but taste different.


In this experiment, I compared the behavior of a rye flour starter I built from scratch with a rye flour starter I converted from my five-year old starter [originally created with all purpose flour] which has been fed many different wheat flours over the years. I baked with these two starters at the four-week and six-week marks and during that time I discarded and fed the starters every few days (with one week-long break) with the same home-milled, whole grain rye flour and I stored them in the refrigerator when they weren’t actively doubling after a feed.

Usually when I do an experiment, my results are in the ballpark of what I had predicted, but this experiment surprised me. After six weeks, the two starters had been discard-fed between 15 and 20 times, and they’re still different colors and have different aromas. Moreover, they make breads that taste different, even though I’ve synced the starters completely in terms of ripening speed, dough leavening strength at warm and cold temperatures, and final loaf appearance.

The rye from “Scratch” starter is grayer in color, fruitier in aroma, and when mature, it feels thicker when stirred. It also makes a bread that most of my taste testers preferred. The rye “Convert” from all purpose flour starter is pinker in color, has a sharper, slightly acetone aroma, and when mature, it feels looser when stirred. It makes a bread that my taste testers enjoyed but found to be less flavorful. (See the conclusion below for more taste testing details.)

Spoiler: These results indicate that the sourdough starter microbiome may be significantly determined by the population of microbes in the initial flour used to create the starter and that this microbiome can remain stable even in the presence of a consistently different feeding flour.


Weeks 1 & 2

Creating a “Convert” to Rye Starter (Tap or roll your mouse on the photos to see the captions)

I fed 6g of all purpose flour starter with 30g of whole grain rye flour and 30g of water (6:30:30 or 1:5:5). After it doubled in 8.5 hours, I refrigerated it overnight. The next day, I discarded down to 6g and again fed 30g each whole grain rye flour and water. This starter, which now contained 0.3g AP flour, doubled in 7 hours. I then refrigerated it for a couple of days. This FAQ explains the math behind the disappearance of the all purpose flour in just two feedings. The amount of AP flour in the Convert starter after multiple feeds is comparable to what might float through the air and land on either starter when I have the starters out on my work space.

Creating a From “Scratch” Rye Starter

I mixed 40g whole grain rye flour and 40g water. After 18 hours, the paste still looked dormant so I stirred it vigorously. At 30 hours, the starter had expanded by about 75% and seemed dormant again. I added more rye flour and water (40g each).The starter then doubled by 42 hours from the initial mixing.

I decided to bake a loaf of bread with this expanded very young starter, and it turned out well. I suspect this initial burst of leavening power was due to the fact that I used home-milled rye flour, which is arguably a more alive than refined flour.

The Scratch starter continued to evolve, however, and was very weak for the next 2-3 feeds. I believe I may have overfed it by discarding and refrigerating too soon. The starter needed more time and feedings at room temperature without discarding for the pH to drop and the final balanced starter microbiome to get established. This took until about day 11, with less but still some refrigeration and discarding.

I didn’t photograph the progress of each feeding, but in the photos below, you can see that during these first couple of weeks, the Convert starter (purple rubber band) and original AP starter (green rubber band) always expanded faster than the Scratch starter (blue rubber band).

Weeks 3 & 4

During these weeks, the Scratch starter began to gain in strength and it became apparent that the two starters were different in color. When the Scratch starter began to exceed the Convert in vigor, I tried to sync the starters up in terms of strength by playing with temperature and feeding ratios.

As the two sourdough starters got closer to syncing up, I decided it was time to do a test bake. I used Breadtopia’s Pain de Campagne recipe, but instead of AP starter and rye flour, I used the Convert and Scratch rye starters. I also didn’t autolyse or laminate any of the doughs, which is part of the process I had originally written into that recipe. For all of the test doughs, I mixed all-in and did two rounds of stretching and folding, and two rounds of coil folding.

Week 4 Test Bake

Week 4 Bake Results

The texture of the Scratch and Convert loaves was similar, but taste testers (two family members) noted in blind taste tests that the Scratch starter bread had “more wheat flavor” and “less sourness.” This was an interesting result on its own, but also unexpected because the Scratch dough spent 7 hours longer in the refrigerator trying to catch up fermentation-wise to the Convert dough. All other things equal, my experience is that more time in the cold usually confers more of a sour flavor, but not in this case.

Weeks 5 & 6

During week 5, I fed the starters once, let them mature, refrigerated them and went away for a week. Upon returning, I discarded both starters down to 30g and fed them 1:1:1 (30g rye flour and 30g water). Below is a photo of the discards, all of which I used in a delicious “just got home from vacation” instant yeast bread. You can see that the starters continue to be two different shades of brown even in different lighting situations.

I refrigerated the two starters at the point you see them in the photo above, and a few days later, I brought them to room temperature and used them in two doughs. This was my week-six test bake, again two pain de campagne breads, with the same formula as the prior test bake, except this time I used rouge de bordeaux as the whole grain red wheat flour.

Week 6 Test Bake

Week 6 Bake Results

Similar to the week-four test bake, the Scratch and Convert loaves of the week-six test bake looked about the same, though this time the similarity was achieved with a virtually identical fermentation duration, as opposed to syncing up the appearance of the dough with differences in bulk fermentation and final proofing time as I did in week 4.

For this test bake, I had six people do blind taste testing. One tester didn’t detect any flavor differences, and the other five preferred the bread leavened with the Scratch rye starter built from rye flour. They described the Scratch bread as having “deeper flavors,” more “huskiness and pepperiness,” and a “better sour” than the Convert rye starter, which had been transformed from an all purpose flour starter. The difference also came through in the aroma of the bread for three of the six testers.

Rye starter built from scratch on left; Rye starter converted from AP starter on the right


For the six-week time period that has passed thus far, this experiment suggests that the microbial composition of these two sourdough starters is not the same despite their being fed the same flour. The sourdough starter built from scratch with rye flour and fed 15-20 times during the test period is grayer in color, mixes with a thicker glue-feel, smells fruitier and less like acetone, and bakes a bread that five of six taste testers preferred. The sourdough starter converted from my original all purpose flour to rye flour and discard-fed 15-20 times is pinker in color, mixes with a thinner liquid-feel, smells less fruity and more like acetone, and bakes a more “one dimensional” and sour bread.

Continuing the experiment for a longer time frame could show an evolution and convergence of the starters or a continued stability of difference. More time and baking is needed to determine this.

It would also be interesting to do a test bake comparing breads made with the Convert starter and with the original all purpose flour starter it grew from (making sure the flour types in each final dough were identical, of course). This could demonstrate whether the Convert has a similar microbial composition as the AP starter or its own microbial composition, not identical to its parent starter or to the Scratch starter.