Microbial community dispersal in sourdough

Understanding how microbes disperse in ecosystems is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about the vectors that may contribute to their migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal among French sourdoughs and flours used to make bread. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analyzed whether flour is a carrier of sourdough yeast and bacteria and studied whether microbial migration occurs between sourdoughs. The microbial community of a collection of 46 sourdough samples, as well as that of the flour from which each was made, was studied by 16S rDNA and ITS1 metabarcoding. No sourdough yeast species were detected in the flours. Sourdough lactic acid bacteria (LAB) were found in only five flour samples, and they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. The species shared between the sourdough and flour samples are commonly found on plants and are not known to be alive in sourdough. Thus, the flour microorganisms did not appear to grow in the sourdough microbial community. Dispersal between sourdoughs was also studied. Sourdoughs shared no yeast ASV, except in few cases where groups of three to five bakers shared some. These results suggest that there is little migration between sourdoughs, except in a few situations where bakers may exchange sourdough or be vectors of yeast dispersal themselves.

Strain-specific interaction of Fructilactobacillus sanfranciscensis with yeasts in the sourdough fermentation

Fructilactobacillus (F.) sanfranciscensis is a key bacterium in traditional (type 1) sourdough fermentations. It typically occurs in combination with the sourdough yeast Kazachstania (K.) humilis or the generalist Saccharomyces (S.) cerevisiae. Previous studies revealed intra-species diversity in competitiveness or dominance in sourdoughs of F. sanfranciscensis, as well as preferences for a life with or without a specific yeast. In this study representative, differently behaving strains were studied in media with different sugars and electron acceptors, and in rye sourdough fermentations in the presence and absence of K. humilis or S. cerevisiae. Strain-specific differences were observed in sugar and organic acids spectra in media, and in sourdoughs with F. sanfranciscensis strains in combination with K. humilis or S. cerevisiae. F. sanfranciscensis TMW 1.1150 proved dominant in the presence and absence of any yeast because it most effectively used maltose. Its maltose fermentation was unaffected by electron acceptors. F. sanfranciscensis TMW 1.2138 was the weakest maltose fermenter and incapable of glucose fermentation, and evidently not competitive against the other strains. F. sanfranciscensis TMW 1.392 was the most versatile strain regarding the utilization of different carbohydrates and its ability to exploit electron acceptors like fructose and oxygen. In sourdoughs without yeasts, it outcompeted other strains. The metabolism of F. sanfranciscensis TMW 1.907 was stimulated in combination with S. cerevisiae. In competitive trials, it was assertive only with S. cerevisiae. The intra-species differences in carbohydrate metabolism can widely explain the differences in their behavior in sourdough fermentation. Interaction between F. sanfranciscensis and the yeasts was strain specific and supposedly commensal with K. humilis and rather competitive with S. cerevisiae.

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

Sourdoughs harbor simple microbial communities usually composed of a few prevailing lactic acid bacteria species (LAB) and yeast species. However, yeast and LAB found in sourdough have been described as highly diverse. Even if LAB and yeast associations have been widely documented, the nature of the interactions between them has been poorly described. These interactions define the composition and structure of sourdough communities, and therefore, the characteristics of the final bread product. In this study, the nature of the interactions between strains of two commonly found sourdough yeast species, Kazachstania humilis and Saccharomyces cerevisiae, and lactic acid bacteria isolated from sourdoughs has been analyzed. Population density analysis showed no evidence of positive interactions, but instead revealed neutral or negative asymmetric interaction outcomes. When in coculture, the yeasts´ population size decreased in the presence of LAB regardless of the strain, while the LAB´s population size was rarely influenced by the presence of yeasts. However, a higher maltose depletion was shown in maltose-negative K. humilis and maltose-positive obligately heterofermentative LAB cocultures compared to monocultures. In addition, tested pairs of obligately heterofermentative LAB and K. humilis strains leavened dough as much as couples of LAB and S. cerevisiae strains, while K. humilis strains never leavened dough as much as S. cerevisiae when in monoculture. Taken together, our results demonstrate that even if higher fermentation levels with increased maltose depletion were detected for K. humilis and obligately heterofermentative LAB pairs, these interactions cannot be ecologically classified as positive, leading us to rethink the established hypothesis of coexistence by facilitation in sourdoughs.