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Publication Impact of process parameters on the sourdough microbiota, selection of suitable starter strains, and description of the novel yeast Cryptococcus thermophilus sp. nov.(2013) Vogelmann, Stephanie Anke; Hertel, ChristianThe microbiota of a ripe sourdough consists of lactic acid bacteria (LAB), especially of the genus Lactobacillus, and yeasts. Their composition is influenced by the interplay of species or strains, the kind of substrate as well as the process parameters temperature, dough yield, redox potential, refreshment time, and number of propagation steps (Hammes and Gänzle, 1997). As taste and quality of sourdough breads are mainly influenced by the fermentation microbiota, intense research has been focused on determination of sourdough associated species and search for new starter cultures. In recent years, economic competition pressure and new consumer demands have led to steady research for new cereal products, especially with health benefit or for people suffering from celiac disease. For these reasons, alternative cereals like oat and barley (both toxic for celiac disease patients) as well as the celiac disease compatible cereals rice and maize, sorghum and millets, the pseudocereals amaranth, quinoa and buckwheat as well as cassava got into the focus of interest. However, information about the microbiota of sourdoughs fermented with buckwheat, amaranth, quinoa, oat or barley is not available except for the following recent studies: a study about the microbiota of amaranth sourdoughs by Sterr et al. (2009), a study about barley sourdough by Zannini et al. (2009), a study about oat sourdoughs by Huettner et al. (2010) and a study about buckwheat and teff sourdoughs by Moroni et al. (2011). The microbiota of sourdoughs from the other mentioned cereals as well as cassava was multiply characterised but not systematically. Fermentation conditions were partly not clearly defined, and identification of species was often based on physiological criteria only, known to be insufficient for the exact classification of LAB. Thus, in this thesis, the influence of the process parameters substrate, temperature, refreshment time, amount of backslopping dough as well as the interplay between the different species or strains were examined and potential starter strains were selected. In Chapter III, the effect of the substrate on the sourdough microbiota was examined and suitable starter cultures for fermentation of non-bread cereals and pseudocereals were selected. Eleven different flours from wheat, rye, oat, barley, millet, rice, maize, amaranth, quinoa, buckwheat and cassava were inoculated with a starter mixture containing numerous LAB and yeasts. Sourdoughs were fermented at 30 °C and refreshed every 24 hours until the microbiota was stable. Species were identified by PCR-DGGE as well as bacteriological culture and RAPD-PCR, followed by 16S/26S rRNA sequence analysis. In these fermentations, the dominant yeast was Saccharomyces cerevisiae; Issatchenkia (I.) orientalis was only competitive in the quinoa and the maize sourdough. No yeasts were found in the buckwheat and the oat sourdough. The dominant LAB species were Lactobacillus (L.) paralimentarius in the pseudocereal sourdoughs, L. fermentum, L. helveticus and L. pontis in the cereal sourdoughs, and L. fermentum, L. plantarum and L. spicheri in the cassava sourdough. Competitive LAB and yeasts were inserted as starters for a further fermentation using new flours from rice, maize, millet and the pseudocereals. After ten days of fermentation, most of the starter strains were still dominant, but L. pontis and L. helveticus could not compete with the other species. It is remarkable that from the numerous starter strains which all were adapted to or isolated from sourdoughs, only a few were competitive in these fermentations; but if, then in most cases in a lot of different flours. In Chapter IV, the effects of the exogenous process parameters substrate, refreshment time, temperature, amount of backslopping dough as well as competing species on the two microbial associations L. sanfranciscensis ? Candida (C.) humilis and L. reuteri ? L. johnsonii ? I. orientalis were examined. Both associations had previously been found to be competitive in sourdough (Kline and Sugihara, 1971a; Nout and Creemers-Molenaar, 1987; Gobbetti et al., 1994a; Garofalo et al., 2008; Böcker et al., 1990; Meroth et al., 2003a). 28 sourdough batches were fermented under defined conditions until the microbiota was stable. Dominant LAB and yeasts were characterized by bacteriological culture, RAPD-PCR and 16S/26S rRNA gene sequence analysis. The process parameters for the association L. sanfranciscensis ? C. humilis could be defined as follows: rye bran, rye flour or wheat flour as substrate, temperatures between 20 and 30 °C, refreshment times of 12 to 24 hours and amounts of backslopping dough from 5 to 20 %. In addition, the association was predominating against all competing lactic acid bacteria and yeasts. The association L. reuteri ? L. johnsonii ? I. orientalis was competitive at temperatures of 35 to 40 °C, refreshment times of 12 to 24 hours and the substrates rye bran, wheat flour and rye flour, but only with sufficient oxygen supply. Cell counts of I. orientalis fell rapidly under the detection limit when using high amounts of doughs (small ratio of surface to volume) and refreshment times of 12 hours. The fermentations depicted in Chapter III and IV give new information about the influence of process parameters on the sourdough microbiota. The studies show that the sourdough microbiota is markedly influenced by the process parameters and kind and quality of substrate. The competitiveness of a single LAB or yeast is strain specific. Interactions between microorganisms also play an important role. However, for the search for suitable starter strains, it would be beneficial to know the reasons, why a single LAB or yeast strain is better adapted to specific process parameters or substrates than others. One of the starter sourdoughs used for fermentation I described in Chapter III was a sourdough made from cassava flour, inoculated with several LAB. No yeast had been inserted, but several yeasts were isolated from the ripe sourdough, which are supposed to originate from the cassava flour. An unknown yeast species constituted 10 % of the isolated yeasts which is described as novel species Cryptococcus thermophilus sp. nov. in Chapter V. This yeast is characterized by budding on small neck-like structures, no fermentative ability, growth at 42 °C and without vitamins, a major ubiquinone of Q-10, as well as the production of green or blue fluorescent substances in the growth medium. It is distinct from related species by the ability to assimilate raffinose and cadaverine, the inability to assimilate soluble starch, xylitol, galactitol, butane-2,3-diol, sodium nitrite and lysine, and the inability to produce starch-like substances. The closest relatives are the yeasts belonging to the Cryptococcus humicola complex.Publication Isolierung universell einsetzbarer und mikrobiologisch stabiler Sauerteigstarterkulturen durch spontane Fermentationen mit Amaranth.(2009) Sterr, Yasemin Arzu; Schmidt, HerbertSpontaneous fermented sourdoughs prepared from five amaranth flours were screened for the presence of lactic acid bacteria (LAB) that predominate the autochthonous microbiota and thus may be suitable as starter cultures. The doughs were fermented with daily backslopping on the laboratory scale for 10 days with a dough yield of 200 at 30°C. Every 24 hours, the pH-values and total titratable acidity degrees were determined and samples were analyzed for the presence of LAB and yeasts by cultural methods. The identity of the isolates was traced during the fermentation with RAPD-PCR and two different primers, and the strains were identified by sequence analysis of the 16S rDNA genes. The strains Lactobacillus plantarum RTa12, L. sakei RTa14, and Pediococcus pentosaceus RTa11 were selected and applied as starters in further laboratory fermentations. All strains were predominant in repeated experiments, both, as single strains and in combination. During the first 24 h, L. plantarum RTa12 and P. pentosaceus RTa11 grew quite similar. The pH-value dropped earlier with P. pentosaceus RTa11, while both strains gave the same pH-values after 10 h of fermentation. In the challenge test with the autochthonous mikrobiota both strains overgrew the other LAB of the spontaneous fermented dough within the first eight hours, and were therefore considered dominant over the resident microbiota. Influences of the incubation temperature on the fermentation characteristics were mainly assessed in the viable cell counts, the pH-values and the titratable acidity degrees at 25°C. The pH-values for both strains were at high incubation temperatures (30 and 35°C) during the fermentation lower than at 25°C, respectively. However, after 24 h of fermentation both strains reached a pH-value of approximately 4.0 after 24 h. Further sugar, organic acid, mannitol and ethanol profiles of fermented doughs were determined with HPLC. Mainly analyzed metabolites in the doughs were glucose, sucrose, lactate, and acetate. To compare the potential starter cultures with commercial available startercultures, fermentations with two industrial startercultures were performed for 24 h at 30°C and a dough yield of 200. Both strains were able to compete with the commercial available starter cultures concerning viable cell counts, total titratable acidity and pH-values. Because of the dominance of both strains in sourdough fermentations with amaranth, the ability for acidification in a short time, the capacity to compete with the autochthonous mikrobiota, the robustness against lesser effects of the environment, e. g. variation of the temperature, and at least because of the ability to compete with commercial available startercultures, thus, the characterized strains L. plantarum RTa12 and P. pentosaceus RTa11 are interesting candidates as starter cultures for amaranth sourdoughs.Publication Mikrobiologische und biochemische Analyse der Fermentationseigenschaften von Lactobacillus paralimentarius AL28 und Lactobacillus plantarum AL30 in Sauerteigen aus Pseudozerealien(2011) Vogel, Antje; Schmidt, HerbertPseudocereals are absent of gluten and therefore are important for people having a gluten-intolerance. Today no commercial starter cultures are available for sourdough fermentations with pseudocereals. This PHD-Thesis shows results of the characterisation of L. paralimentarius AL28 and L. plantarum AL30 concerning an application in pseudocereal sourdoughs. The fermentation properties of the strains, applied as single strains and in combination, were assessed in laboratory scale fermentations with amaranth and buckwheat. The fermentation studies were performed with a dough yield of 200 and over a period of two to ten days at 30°C with daily refreshment step. The investigated strains acidified the sourdoughs fast within the first two propagation steps as single strains as well as in combination (approximately pH 4). In amaranth higher total titratable acidity (TTA) -values (TTA between 25 and 30) were measured than in buckwheat (TTA of 20). 16S rDNA / 28S rDNA-PCR sequencing and RAPD-PCR were applied to determine the bacterial and eucaryotic species affiliation, respectively, and to trace specific strains during the fermentation process. The analysed strains competed against the autochthonous microbiota with the result of suppression the majority of yeasts and moulds as well as strains of their own species within the first 12 h of sourdough fermentation. They also suppressed an autochthonous microbiota grown up to 10^8 cfu/g sourdough. Single strains as well as the combination of both strains dominated the microflora in all tested flours / fermentation batches. Both strains displayed reproducible results concerning their over-all fermentation characteristics. L. paralimentarius AL28 and L. plantarum AL30, respectively, dominated the LAB viable counts in all flours after 10 days of fermentation as single strains (>/= 68 % and >/= 98 % of LAB, respectively) as well as in combination. In the latter case strain L. plantarum AL30 was especially competitive in buckwheat (AL28:AL30 = 1:1), more than in amaranth (AL28:AL30 = 4:1). The strains were characterised by their short lag-phase of