Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour

Abstract

Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales , mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae , known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity.

Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs

“…Sourdough is a mix of flour and water naturally fermented by bacteria and yeasts. Sourdough yeast density ranged from 8.1 10 4 to 5.8 10 8 CFU per gram of sourdough, with a mean value of 2.9 10 7 CFU per gram, as commonly found in sourdoughs from all over the world [1, 17, 46, 47]. We isolated 20 to 40 yeast strains from each sourdough and identified species using ITS sequence as well as other barcodes when needed (see M&M section).…”

Interactions between Kazachstania humilis Yeast Species and Lactic Acid Bacteria in Sourdough

“…These microbial communities are quite simple, usually harboring one effective yeast species and two effective LAB species [6]. However, a rather high microbial diversity has been described when considering different sourdoughs all over the world; more than 60 LAB species and 30 yeast species have been described so far [7][8][9][10][11][12][13][14][15][16]. Most described LAB species belong to the genus Lactobacillus, and most yeast species to the genera Saccharomyces, Kazachstania, Wickerhamomyces, Torulaspora, and Pichia.…”

“…Pentose may be fermented by the phosphogluconate pathway [17,18]. The most widespread yeast species in sourdough are Saccharomyces cerevisiae, Kazachstania humilis (previously named Candida humilis), Kazachstania exigua, Pichia kudriavzevii, and Torulaspora delbrueckii [6,14,16]. These yeast species all ferment hexoses in the absence and presence of oxygen, and thus, convert carbohydrates into ethanol, carbon dioxide, and acetic acid.…”

Evidence for two main domestication trajectories inSaccharomyces cerevisiaelinked to distinct bread-making processes

“…The collection of strains analysed is presented on Tables S1, S5, S8. One hundred and twenty-nine strains were collected from sourdoughs in France as previously described [42,60]. Twenty sourdough strains from Belgium isolated by [61] were kindly provided by the Belgium MUCL collection.…”

“…The yeast species found in sourdough mainly belong to the genera Saccharomyces sensus stricto, Kazachstania, Pichia, Torulaspora. Worldwide, S. cerevisiae is the most widespread species found in sourdoughs [40] made by bakers, but also in sourdough made by farmersbakers [41,42]. It can be found as the dominant species in sourdough, even in bakeries where no industrial starter is used, suggesting that the species may colonize a sourdough from the bakery's environment or the baker's hands [43].…”