Artisanal and farmers bread making practices differently shape fungal species diversity in French sourdoughs

Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. However, there is still a lack of knowledge about the factors that may influence food microbial diversity, notably in fermented foods. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider diversity of microbial species. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyse French bread making practices and describe fungal communities in naturally fermented sourdough. Bread making practices were clustered in a farmer practices’ group and an artisanal practices’ group. Surprisingly, the well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs and other yeast species of the closely related Kazachstania genus were frequent. Bread making practices were found to drive the distribution of these species. The differences in fungal communities were associated with variation in sourdough acidity, maltose concentration and hydration. Overall, our results showed that preserving bread making practices diversity allows the preservation of a higher taxonomic and functional diversity in microbial communities.