Microbial Ecology of Fremented Foods: Case Studies from Industrialized and Household Productions

Research output: Book/ReportPh.D. thesisResearch

Fermented food and beverages make up an important part of today’s food culture, which is highlighted by the broad variety of marketed products in both industrialized and developing countries. The diversity of fermented foods arises from cultural differences in food handling. To improve quality and safety of fermented products, all fermentation technologies aim at promoting growth of beneficial microorganisms, while inhibiting contaminants and pathogenic microorganisms. Enzymatic activities of microorganisms convert major and minor components in raw materials into fermented foods. Fermentations are often driven by complex communities that interact among each other leading to microbial successions. Hence, intricate ecological processes underlie food fermentations. Dissecting the mechanisms of microbial community formation and interactions are of major importance for understanding the microbial ecology and for optimizing the processing of fermented foods and beverages. The main purpose of this thesis was therefore to apply a comprehensive approach to extend the understanding of microbial ecology in fermented foods. Cheese brines and surface ripened semihard Danbo cheese produced at industrial scale in Denmark, spontaneously fermented milk (lait caillé), and spontaneously fermented cereal dough (mawè) produced at traditional household scale in Burkina Faso and Benin, were selected as examples for analysis. Further, literature surveys on yeast occurrence and their importance in indigenous sub-Saharan African fermented foods and beverages, as well as the impact of microbial quorum sensing on the quality of fermented foods, were carried out. Based on the literature surveys, a large diversity of yeast species was identified in indigenous subSaharan African fermented foods and beverages. Among these, few were predominating the fermentations, while the majority were present in low abundance. Moreover, in several of the products, successions were reported and generally, a larger number of yeast species initiated the fermentations, while far fewer completed them. Further, several different interaction mechanisms between microorganisms in the consortium were reported. Yeasts have been documented to influence a number of quality aspects in sub-Saharan African fermented foods and beverages, including aroma compound formation, phytic acid degradation, increasing folate content, aflatoxin binding and degradation of cyanogenic compounds, as well as displaying probiotic properties. In the second literature survey, quorum sensing was found to be widespread among food-borne microorganisms and present in both pro- and eukaryotes. Several traits have been reported to be controlled by quorum sensing in microorganisms isolated from fermented foods and beverages. Especially traits such asbiofilm formation, acid stress tolerance, bacteriocin production, competence, morphological switches, adhesion and gliding motility as well as oriented colony growth. In several fermented foods, including fermented vegetables, sourdough, dairy products, wine, and so on, quorum sensing has been reported for microorganisms involved in the fermentations, suggesting that quorum sensing plays a role in the fermentation of these fermented foods. In the experimental part, it was established that application of both culture-dependent and -independent techniques increased the number of identified microorganisms in Danish cheese brines, especially for the less abundant bacteria and yeasts. Similarly, a more in-depth detection of the less abundant microorganisms in industrially processed Danish surface ripened semi-hard Danbo cheese was achieved by pyrosequencing. The microbial successions observed during processing of surface ripened semi-hard Danbo cheese, related to the different processing steps, i.e. acidification, brining, smearing and ripening. At traditional household scale in West Africa, the microbial successions correlated with the gradual acidifications occurring during the spontaneous fermentation of milk into lait caillé and cereals into mawè, respectively. Further, in mawè the type of cereal (i.e. sorghum or maize) and soaking of cereal grains in boiling water influenced the species biodiversity. Of the predominant species isolated from mawè, the most abundant strain clusters were ubiquitously present, while few were identified only at a single production site. Especially raw material, processing method and production site affected the strain diversities, suggesting a strong link between particular strains and the individual processing sites. Finally, it was demonstrated that yeast strains isolated from mawè were affected in a species-, strain- and cell dependent manner when exposed to the intrinsic stress factors of spontaneously fermented cereal doughs, i.e. low pH, ethanol, lactic acid and acetic acid. In conclusion, the experiments and literature surveys carried out showed that application of comprehensive identification techniques extended the number of identified species. The observed microbial successions could be related to the processing conditions, while the microbial biodiversity at both species and strain level was influenced by processing conditions and raw materials. Finally, yeast viability was affected in a species-, strain- and cell dependent manner when exposed to the intrinsic stress factors of cereal dough fermentations. The obtained knowledge contributes toward linking patterns of microbial diversity within communities to the ecological processes generating those patterns. This knowledge is a key driver for developing new starter cultures for both industrialized- and house scale productions and for controlling fermentation conditiona to ensure improved quality and increased safety of the fermented foods around the world.
Original languageEnglish
PublisherDepartment of Food Science, Faculty of Science, University of Copenhagen
Publication statusPublished - 2019

ID: 223825308