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Microbial terroir

How to think of community assembly in fermented foods

You might be familiar with the concept of terroir, from the French meaning soil or land. In winemaking, it is often described as ‘a sense of place,’ a reflection of how the soil, climate, and topography impacted the grape, fermentation, and ultimately the final quality of the product.

The idea of terroir can extend to other fermented foods. While using the term terroir perpetuates the false francocentric history of wine and is, quite frankly, unnecessarily pretentious, we can use terms like origin or typicality (see Roberta Raffaetà) to describe how the starter ingredients and environment of production affected the final product.

But what role do microbes play in shaping terroir? Dr. Michael Gänzle from the University of Alberta, has published extensively on identifying the microbial origins of the foods we ferment and eat. He describes terroir as “relevant with respect to the choice and quality of the raw material, the product formula, and the production processes but not with respect to the composition of fermentation microbiota” (Gänzle, 2019). We must look at microbial ecology to describe the way communities are shaped in food fermentation.

α-diversity: the number and distribution of microbes in one sample

β-diversity: the measure of similarity or difference in microbial populations when comparing multiple samples

γ-diversity: the measure of overall diversity across a wide geography
α-diversity: you sequence your sourdough starter and find that S. cerevisiae makes up 50% of all microbes, L. plantarum makes up 15%, and the rest are a mix of other bacteria and yeast, each no more than 2%. What kind of microbes are present and what % they make of the total number of microbes in your sourdough is your  α-diversity. 

β-diversity: you sequence another sourdough starter, and compare the type and number of microbes you find in this second starter to the first starter. The similarities and differences in the type of microbe and abundance of each microbe between the two starters will be your β-diversity.

γ-diversity: you sequence all sourdough starters across the US, and find that there are microbes common to all sourdough, and some microbes that are unique to certain regions in which the sourdough is made. The similarities and differences in the type of microbe and abundance of each microbe across all sampled sourdoughs will be your γ-diversity.

Formation of a new species over the course of evolution
Microbial speciation occurs on the scale of millions of years, while food fermentation practice has occurred on a much shorter time scale (~14,000 years), making the concept of speciation almost irrelevant to microbial food fermentation. However, strains (a subtype within a species) can have specific traits that are adaptive to their specific environment-- while they are the same species, the strains of S. cerevisiae that produces good sourdough are not the same strain of S. cerevisiae that produces good wine.

Random event that might shape your α-diversity
You are preparing to make a load of sourdough and are doing the inital fermentation step. It’s a very hot day, which leads to some strains in your sourdough to grow more rapidly, shifting the typical α-diversity and leading to a different flavor profile than you expected.

Movement of microbes across an environment
Important for spontaneous fermentation. Where are the microbes driving fermentation coming from? While making your sourdough from scratch, microbes will be coming from your flour and water, from the container and spoon you are mixing them with, from your hands and breath, or from the air.

Microbes with the greatest community fitness will thrive in the ferment at a higher rate compared to lower fitness members
Factors like salinity, oxygenation, temperature, humidity, acidity, and nutrient content of the starting ingredients will all affect which microbes will grow best and dominate the community, or be “selected for.” Fermentation as a practice is built on selecting for microbes that we consider favorable for their contribution to the final flavor and texture of food. 


Gänzle, Michael. "Fermented foods." Food microbiology: fundamentals and frontiers (2019): 855-900.

Raffaetà, Roberta. "Microbial antagonism in the Trentino Alps: negotiating spacetimes and ownership through the production of raw milk cheese in Alpine high mountain summer pastures." Current Anthropology 62.S24 (2021): S323-S332.
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