Abstract
Fermented food are an important part of our diet and of gastronomical cultures around the globe. The microorganisms composing them develop in an environment controlled by humans and can thus be domesticated. Because the microbial communities of fermented foods are generally relatively simple, they can be good models for microbial ecology and domestication studies.My PhD focuces on the microbial communities of sourdough bread and of a traditional fermented milk from Brittany region called Gwell. These two products are maintained by back-slopping, i.e. a part of a previous production is used to inoculate the next one. They are thus maintained by the producers, sometimes during several years.The first part of my thesis consisted in studying the dispersal of microorganisms. I showed that the flour added to sourdough during the back-sloppings did not introduce new fermenting microorganisms into the mature sourdough, and that the exchange of ferments between Gwell producers resulted in two lineages of Gwell with distinct microbial communities.The second part of my thesis focused on the stability of microbial community during their maintenance by producers. My results showed that most bakers maintained the same dominant fermentative yeast species in their sourdough over years, as long as they did not change bakery, bakers, or initiate a new sourdough. With respect to Gwell, we conducted an in-farm experimental evolution assay with three Gwell producers. We showed that an increased frequency of back-slopping resulted in a faster acidification of the Gwell, because the bacterial species mainly responsible for the acidification in Gwell was more resistant to cold shocks and was thus favored. Our results further suggested that Gwell bacteria adapted over the long term to the back-slopping practices of the producer.My thesis was conducted using a participatory approach, with producers taking part in one or more steps of the research process, from the development of the research questions to the analysis of the results. This approach allowed us to share our empirical and scientific knowledges on fermented food. These exchanges took the form of training session, meetings for the preparation of the experimentation, synthesis of results, or informal exchanges, as the research process progressed.