Proefschrift Uppsala, Swedish University of Agricultural Sciences. / Includes bibliographical references.

Les potentialités liées aux cultures mixtes de micro-organismes sont immenses et ouvrent de vastes possibilités pour l’innovation dans les bioprocédés. Cependant, étant donné la complexité des phénomènes régulant la physiologie d’un seul micro-organisme, leur mise en oeuvre en culture mixte est d’autant plus difficile à maîtriser que des interactions entre ces micro-organismes viennent s’ajouter. Le travail présenté dans ce manuscrit est une étude d'un couple de levures oenologiques constitué de Saccharomyces cerevisiae et de Torulaspora delbrueckii. Son objectif est d'acquérir des informations expérimentales afin d’analyser et in fine modéliser l'évolution des cultures pures et des cultures mixtes. L'analyse des données expérimentales acquises lors des cultures pures de chaque levure a permis de quantifier l'effet favorable de la concentration initiale d'azote assimilable sur la croissance et la vitesse de fermentation des deux levures. Elle a aussi mis en évidence une prolongation de la phase de latence de T. delbrueckii induite par une augmentation des facteurs anaérobies. Les cultures mixtes ont été réalisées en présence et en absence de membrane de séparation permettant ainsi d'observer les effets du contact physique sur l'évolution des cocultures. Le contact physique influence la dynamique des populations. En culture mixte, S. cerevisiae domine T. delbrueckii dans un milieu synthétique classique. Une augmentation de la concentration initiale de facteurs anaérobies inverse complètement cette domination. L'analyse des résultats expérimentaux nous a orienté vers le développement d'un modèle «stoechio-cinétique» structuré dans lequel l'azote assimilé par la levure se répartit en deux compartiments: le compartiment constitutif et le compartiment de stockage. Ce modèle a permis une représentation fidèle des cinétiques observées en culture pure. La prise en compte des interactions s'est faite en intégrant la compétition pour les substrats, les interactions indirectes et les interactions directes. L'ensemble des hypothèses émises lors de ce travail de modélisation souligne la nécessité d'approfondir les connaissances scientifiques concernant le métabolisme deT. delbrueckii en anaérobiose stricte et l'effet des facteurs anaérobies sur les interactions microbiennes.

Reproduction de : Thèse de doctorat : Microbiologie : Toulouse 3 : 2006. / Titre provenant de l'écran-titre. Bibliogr. p. 315-345.

Les potentialités liées aux cultures mixtes de micro-organismes sont immenses et ouvrent de vastes possibilités pour l’innovation dans les bioprocédés. Cependant, étant donné la complexité des phénomènes régulant la physiologie d’un seul micro-organisme, leur mise en oeuvre en culture mixte est d’autant plus difficile à maîtriser que des interactions entre ces micro-organismes viennent s’ajouter. Le travail présenté dans ce manuscrit est une étude d'un couple de levures oenologiques constitué de Saccharomyces cerevisiae et de Torulaspora delbrueckii. Son objectif est d'acquérir des informations expérimentales afin d’analyser et in fine modéliser l'évolution des cultures pures et des cultures mixtes. L'analyse des données expérimentales acquises lors des cultures pures de chaque levure a permis de quantifier l'effet favorable de la concentration initiale d'azote assimilable sur la croissance et la vitesse de fermentation des deux levures. Elle a aussi mis en évidence une prolongation de la phase de latence de T. delbrueckii induite par une augmentation des facteurs anaérobies. Les cultures mixtes ont été réalisées en présence et en absence de membrane de séparation permettant ainsi d'observer les effets du contact physique sur l'évolution des cocultures. Le contact physique influence la dynamique des populations. En culture mixte, S. cerevisiae domine T. delbrueckii dans un milieu synthétique classique. Une augmentation de la concentration initiale de facteurs anaérobies inverse complètement cette domination. L'analyse des résultats expérimentaux nous a orienté vers le développement d'un modèle «stoechio-cinétique» structuré dans lequel l'azote assimilé par la levure se répartit en deux compartiments: le compartiment constitutif et le compartiment de stockage. Ce modèle a permis une représentation fidèle des cinétiques observées en culture pure. La prise en compte des interactions s'est faite en intégrant la compétition pour les substrats, les interactions indirectes et les interactions directes. L'ensemble des hypothèses émises lors de ce travail de modélisation souligne la nécessité d'approfondir les connaissances scientifiques concernant le métabolisme deT. delbrueckii en anaérobiose stricte et l'effet des facteurs anaérobies sur les interactions microbiennes. / The potentialities associated with cultures of mixed micro-organisms are tremendous and offergreat opportunities for innovation in bioprocesses. The phenomena regulating the physiology of asingle micro-organism are complicated. Furthermore, the eventual additional interactions between two micro-organisms make their implementation in mixed culture difficult to control. The workpresented in this manuscript is a study of a couple of oenological yeasts composed of Saccharomyces cerevisiae and Torulaspora delbrueckii. Its objective is to acquire experimentaldata in order to analyse and ultimately model the evolution of pure and mixed cultures. The analysis of experimental data acquired during the pure cultures of each yeast enable to quantifythe favorable effect of the initial concentration of assimilable nitrogen on the growth and fermentation rate of the two yeasts. It also shows an extended latency phase of T. delbrueckiiinduced by an increase in anaerobic factors. The mixed cultures were carried out in the presenceand absence of separation membrane in order to observe the effects of physical contact on theevolution of cocultures. Physical contact influences population dynamics. In mixed culture, S.cerevisiae dominates T. delbrueckii in a classical synthetic medium. An increase in the initialconcentration of anaerobic factors completely reverses this domination. The analysis of the experimental results has directed us towards the development of a structured stochiometric andkinetic model in which the nitrogen assimilated by the yeast is partitioned into two compartments:the constitutive compartment and the storage compartment. This model faithfully represents thekinetics observed in pure culture. The consideration of interactions was done by integrating competition for substrates, indirect interactions and direct interactions. All the hypotheses emitted during this modelling work underline the need to deepen the scientific knowledge concerning T.delbrueckii metabolism under strict anaerobic conditions and the effect of anaerobic factors onmicrobial interactions

O crescimento do mercado de cervejas artesanais tem demandado inovações. Uma abordagem que se destaca neste contexto é o uso de leveduras não convencionais em processos controlados de fermentação. Para ter melhores resultados neste cenário é fundamental que o produtor conheça as capacidades e limitações das leveduras que serão utilizadas na produção de cervejas. Assim, este estudo teve como objetivo avaliar características fisiológicas, essenciais e complementares, de uma cepa de Brettanomyces anomalus e uma Torulaspora delbrueckii para a produção de cervejas, comparando-as com duas cepas de Saccharomyces cerevisiae já utilizadas na indústria cervejeira. Avaliou-se o perfil cromossômico das leveduras (cariotipagem), a capacidade de crescimento em diferentes substratos e fontes de carbono, bem como em diferentes concentrações de etanol e compostos de lúpulo, a capacidade de esporulação, floculação, produção de sulfeto de hidrogênio (H2S), formação de espuma e a evolução da fermentação em função do tempo. Foram observadas diferenças entre os padrões cromossômicos das quatro leveduras. A intensidade de produção de H2S foi maior para a B. anomalus (WLP640) quando comparada com T. delbrueckii (WLP603), que foi classificada com a mesma intensidade de produção da S-33 (S. cerevisiae). As duas leveduras não convencionais atenderam às características fisiológicas essenciais para fermentação de cervejas. A B. anomalus foi capaz de metabolizar diversas fontes de carbono, como glicose, frutose, sacarose, maltose, matotriose e celobiose, ao passo que a T. delbrueckii cresceu apenas em glicose, frutose e sacarose, apontando sua potencial aplicação para produção de cervejas com teor alcoólico reduzido ou seu uso em inoculações sequenciais ou co-inoculações com outras leveduras. Ambas apresentaram crescimento em teores alcoólicos de 4% e 8%, ao passo que T. delbrueckii tolerou maior concentração de compostos do lúpulo em relação à B. anomalus, que não foi capaz de crescer em meio com as maiores concentrações combinadas de álcool (8% v/v) e α-ácidos (80 mg/L). Os resultados permitem concluir que as leveduras B. anomalus e T. delbrueckii possuem potencial para a produção de cervejas, desde que seja observada a compatibilidade de suas características fisiológicas com a expectativa acerca das características da cerveja. / The booming in the craft beer market worldwide has demanded innovations to bring up distinctive products. An approach that stands out in this context is the use of non-conventional yeasts in controlled beer fermentation processes. To have better outcomes in this scenario, it is essential that the producer knows the capabilities and limitations of those yeasts. Thus, this study aimed to assess essential and complementary physiological traits of one strain of Brettanomyces anomalus and one of Torulaspora delbrueckii for beer brewing, comparing them with two Saccharomyces cerevisiae strains already used in commercial breweries. The characteristics assessed were chromosome profile (karyotyping technique), growth capacity in different substrates and carbon sources, as well as under different concentrations of ethanol and hop compounds, the capability of sporulation, flocculation, hydrogen sulfide (H2S) production and foam formation and, finally, the fermentation evolution pattern. Differences in the chromosomal profile were observed among the four strains. The potential for H2S production was higher for B. anomalus (WLP640) when compared to T. delbrueckii (WLP603), which had the same potential than S-33 (S. cerevisiae). Both non-conventional yeasts have met the essential physiological traits demanded to carry beer wort fermentation. B. anomalus was able to metabolize many of the assessed carbon sources, as glucose, fructose, sucrose, maltose, maltotriose and cellobiose, while the T. delbrueckii strain was able to grow only in glucose, fructose and sucrose, pointing its potential application for low alcohol beer production, as well as its use in sequential inoculations or co-inoculations with other yeasts. Both showed satisfying growth under alcohol contents of 4% and 8%. T. delbrueckii tolerated higher hop compounds concentration when compared to B. anomalus, that was unable to grow at the highest combined concentrations of ethanol (8% v/v) and α-acids (80 mg/L). The results lead to the conclusion that the yeasts B. anomalus and T. delbrueckii can be explored in beer brewing, provided that an alignment between their physiological traits and the expectations around the beer characteristics are observed.

Made available in DSpace on 2015-03-26T13:51:58Z (GMT). No. of bitstreams: 1 texto completo.pdf: 822133 bytes, checksum: e079e0bf0b7042a8b0741f41174d4120 (MD5) Previous issue date: 2006-05-10 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The physiological and technological parameters important to the development of Direct Vat Set culture of Lactobacillus delbrueckii UFV H2b20 cultivated in Minas Frescal cheese whey were studied. Greater fermentative activity on cheese whey was observed at 40ºC and therefore all bacterial growth experiments were performed at this temperature. Heat shock, 50ºC for 30 minutes, or acid stress, cheese whey with pH 3.5 for 30 minutes, did not affect growth of L. delbrueckii UFV H2b20 on cheese whey. The survival of heat or acid pre-treated cells was assessed after dehydration by lyophilization and spray-drying. Cell survival to either dehydration processes was not affected by acid pre-treatment, whereas heat shock had a deleterious effect on survival. The addition of protective substances (6% mannitol, 1,25% sorbitol, 1,25% monosodium glutamate and mixture of 6% sucrose and 4% trehalose) to cheese whey in which the cells were submitted to lyophilization did not improve cell survival to dehydratation and storage at -80ºC for two months. Cell survival was greater when lyophilization was performed on cheese whey alone. Acid pre-treated cells on cheese whey, pH 3.5 adjusted with HCl, without any further addition, retained higher viable counts after lyophilization and subsequent -80ºC storage. Cell activity recovery in 10% reconstituted skimmed milk was not affected by either heat shock or acid pre-treatment when cells were lyophilized in cheese whey with no additional substances. Spray-dried cultures submitted to acid stress demonstrate recovery comparable to active cells which were not subjected to any condition that could result in cell injury. Those cultures exhibit a high activity even after two months storage at - 20ºC. The hereby presented results demonstrate that the probiotic culture produced in stabilized Minas Frescal cheese whey, pre-treated at pH 3.5, and spray-dried have desirable viability and activity characteristics, and its use can be recommended for the elaboration of milk fermented products containing L. delbrueckii UFV H2b20 cells. / Os parâmetros fisiológicos e tecnológicos de importância para o desenvolvimento de sistema DVS para Lactobacillus delbrueckii UFVH2b20 em soro de queijo Minas Frescal estabilizado foram estudados. A maior atividade fermentativa das células do L. delbrueckii UFV H2b20 em soro de queijo ocorreu a 40ºC. Por essa razão, essa temperatura de incubação foi adotada para a condução dos experimentos. Foi observado que a aplicação de choque térmico, 50ºC por 30 minutos, ou choque ácido, pH 3,5 por 30 minutos, a 40ºC, às células de L. delbrueckii UFV H2b20 não afetaram seu crescimento. Foi avaliado ainda se a aplicação de tais pré-tratamentos afetava a sobrevivência aos processos de desidratação das células por liofilização e spray-drying. Foi observado que o choque ácido não afetou a sobrevivência de L. delbrueckii UFV H2b20 aos dois processos de desidratação avaliados. Por outro lado, o choque térmico teve efeito deletério sobre a sobrevivência das células submetidas aos mesmos processos de desidratação. Para as culturas liofilizadas, foi avaliado se a adição de diferentes soluções protetoras (manitol 6%, sorbitol 1,25%, glutamato monossódico 1,25% e mistura das soluções de sacarose 6% e trealose 4%) exercia efeito sobre a sobrevivência de L. delbrueckii UFV H2b20 à liofilização, bem como durante o período de estocagem das células desidratadas a -80ºC por 2 meses. A sobrevivência das células ao processo de liofilização foi maior quando não se adicionaram substâncias crioprotetoras ao soro de queijo. Maior viabilidade durante o armazenamento a -80ºC foi observada quando as células foram pré-tratadas em soro de queijo pH 3,5, ajustado com HCl e sem a adição de outras substâncias antes da liofilização. Observou-se que os choques térmico ou ácido não afetaram a recuperação imediata em leite desnatado reconstituído a 10% das culturas liofilizadas que não sofreram adição de substâncias protetoras. Nas culturas desidratadas por spray-drying, observou-se que as células de L. delbrueckii UFV H2b20, previamente submetidas ao choque ácido, lograram crescimento comparável ao obtido pelas células ativas que não foram submetidas a qualquer condição que possa causar injúria. Essas culturas permaneceram com elevado número de células, mesmo após 2 meses de estocagem a -20°C. Os resultados obtidos levam à conclusão de que a cultura starter probiótica produzida em soro de queijo Minas Frescal estabilizado, desidratada por spray-drying e previamente submetida ao choque ácido, demonstrou características de viabilidade e atividade mais promissoras, e seu uso pode ser recomendado para a elaboração de produtos lácteos fermentados contendo células do L. delbrueckii UFV H2b20.

Le travail décrit dans cette thèse a commencé avec la découverte d’effets anti-inflammatoires chez certaines souches de L. delbrueckii. Il avait été montré que l’effet anti-inflammatoire est souche-dépendant, et implique l’action de protéines exposées à la surface de la bactérie. Dans le but d’identifier l’effecteur bactérien à l’origine de l’effet immuno-modulateur, 8 souches de L. delbrueckii ont été sélectionnées. Deux de ces souches sont à fort effet anti-inflammatoires, et les 6 restantes sont à effet faible ou intermédiaire. Pour l’identification des protéines potentiellement responsables pour l’effet anti-inflammatoire, des études de génomique et transcriptomique comparatives des 8 souches de L.delbrueckii ont été entreprises, ainsi qu’une étude comparative du protéome de surface bactérienne.La première partie de cette thèse décrit les résultats de finition du génome d’une des deux souches hautement anti-inflammatoires. Cette étape a révélé que la partie manquante de la séquence génomique était principalement composée de séquences répétées de type séquences d’insertions (IS), dont le nombre s’avère particulièrement élevé.La deuxième partie de la thèse décrit une étape de valorisation des données génomiques à travers une étude comparative entre souches de la ssp. lactis et souches de la ssp. bulgaricus. Cette étude révèle que les deux ssp. de L. delbrueckii évoluent en adaptation au milieu lait. Toutefois, la ssp. bulgaricus semble avoir atteint un stade d’adaptation plus avancé que celui de la ssp. lactis. L’adaptation des deux ssp. à leur environnement se fait principalement par un phénomène de perte spontanée de gènes devenus superflus.Une étude plus avancée de la structure génomique des deux ssp. révèle deux nouveaux aspects des différences de structure génomique. Tout d’abord, au sein du core génome des deux sous-espèces, les évènements d’échange génétique et recombinaison ont contribué plus à la diversité au sein de la ssp. lactis qu’à la diversité chez la ssp. bulgaricus. Ensuite, une structure inversée répétée de grande taille, rarement observée dans les génomes bactériens, s’avère caractéristique de la ssp. bulgaricus. La troisième partie de thèse décrit les trois approches comparatives menées dans le but d’identifier les protéines bactériennes à l’origine de l’effet anti-inflammatoire. Au bout de ces études, nous avons sélectionné 56 gènes candidats, dont 41 ont été clonés dans un système d’expression hétérologue. Pour l’instant, 17 clones d’expression ont été testés in vitro pour leur potentiel immuno-modulateur. Les résultats préliminaires ont permis l’identification d’une protéine à effet anti-inflammatoire. / The work described in this thesis began with the discovery of anti -inflammatory effects in certain strains of L. delbrueckii. The anti- inflammatory effect had been shown to be strain - dependent, and implicate the action of bacterial surface exposed proteins.In order to identify the bacterial effector responsible for the immunomodulatory effect, eight strains of L. delbrueckii were selected. Two of these strains have a strong anti -inflammatory effect, whereas the remaining strains have a weak to intermediary effect. To identify proteins that may be responsible for the anti- inflammatory effect, comparative genomic and transcriptomic studies of the 8 L.delbrueckii strains were conducted, as well as a comparative study of the bacterial surface proteome.The first part of this thesis describes the genome finishing of one of the highly anti- inflammatory strains. This step revealed that the missing part of the genome sequence was mainly composed of repeated sequences such as insertions sequences (IS), that were present in a particularly high number.The second part of the thesis describes the valorisation of genomic data through a comparative study between ssp. lactis strains and ssp. bulgaricus strains. This study reveals that both L. delbrueckii ssp. are evolving in adaptation to the milk environment. However, the ssp. bulgaricus appears to have reached a more advanced stage of adaptation than the ssp. lactis. The adaptation of both ssp. to their environment is primarily a phenomenon of spontaneous loss of genes that have become superfluous. A more detailed study of the genome structure of the two ssp. reveals two important differences. Firstly, within the L. delbrueckii core genome, genetic exchange and recombination contributed much more to the ssp. lactis diversity than to the ssp. bulgaricus diversity. Furthermore, a large inverted repeat structure, rarely observed in bacterial genomes, appears to be characteristic of the ssp. bulgaricus.The third part of the thesis describes the three comparative approaches used to identify bacterial proteins responsible for the anti- inflammatory effect.We selected 56 candidate genes, of which 41 were cloned in a heterologous expression system. So far, 17 expression clones were tested in vitro for their immunomodulatory potential. The preliminary results allowed the identification of one protein with anti-inflammatory effects.

Phosphofructokinase (PFK) from the lactic acid bacterium Lactobacillus delbrueckii subspecies bulgaricus (LbPFK) is a non-allosteric PFK with weak binding affinity for both the allosteric ligands phospho(enol)pyruvate (PEP) and magnesium adenosine diphosphate (MgADP). PEP and MgADP bind to the same allosteric binding site but exhibit opposite effects, PEP acting as an inhibitor and MgADP an activator. In 2005, Parichatttanakul, et al. solved the first crystal structure of LbPFK to 1.87 A resolution and allowed for a structural comparison of LbPFK to the allosteric forms of PFK from E. coli (EcPFK) and Bacillus stearothermophilus (BsPFK). Two additional structures of LbPFK have been determined with the first having phosphates bound at the four active sites and four allosteric sites solved to 2.20 A resolution. The second structure solved to 1.83 A resolution contains phosphates at all eight sites with the addition of the substrate fructose-6-phosphate (F6P) in the active sites. These structures are similar to the published sulfate-bound LbPFK structure. Overall, the secondary, tertiary and quaternary structure is conserved with the exception of the residues in the allosteric site. E55, H59, S211, D214, H215 and G216, as well as the long cassettes of residues 52-61 (PFKs1) and 206-218 (PFKs2) were mutated to the corresponding residue/residues in Thermus thermophilus PFK (TtPFK). PFKs1 and PFKs1 were also combined to form PFKs1s2. The single mutations along with PFKs1 and PFKs2 showed no enhancement in PEP binding, but PFKs1s2 enhanced PEP binding 10-fold with no change in MgADP binding compared to LbPFK. D12, located along the active site interface 15 A away from the allosteric site, was mutated to an alanine and exhibited enhanced binding 9-fold for both PEP and MgADP to the allosteric binding site. A crystal structure of D12A was solved to 2.30 A resolution with sulfate bound to all eight binding sites, and showed no major changes in secondary, tertiary or quaternary structure when compared to the sulfate-bound wild-type LbPFK structure. Combining D12A with PFKs1s2 (PFKs1s2/D12A) further enhanced PEP binding with a 21-fold tighter binding compared to LbPFK with MgADP binding being similar to D12A. PEP inhibition was also quantitated in PFKs1s2/D12A with a Q_ay = 0.007 plus/minus 0.0008. Coupling between PEP and F6P in PFKs1s2D12A is 2-fold stronger than the coupling measured in EcPFK and 7-fold stronger than the coupling measured in BsPFK. The coupling measured in PFKs1s2D12A is the first measured in any of the LbPFK variants.

Soy flour was inoculated with Lactobacillus delbrueckii ssp. lattis R0187, and incubated for 8 h, to evaluate the protein hydrolysis and identify peptides generated by this fermentation, and the impact on ACE and trypsin inhibitory activities. Aqueous protein extracts prepared from different fermentation time periods showed a decrease in soluble protein content (from 2.83 to 0.02 mg/mL), while soluble inorganic nitrogen and free amino acid contents increased (from 0.029 to 0.062% w/w, and from 0.75 to 0.90% w/w, respectively). The protein extracts were analyzed by SDS-PAGE; proteolysis was observed after 5 h incubation of inoculated soy flour, suggesting that glycinin, beta-conglycinin, and trypsin inhibitors, were hydrolyzed. Peptides were isolated by tricine-SDS-PAGE, and analyzed by MS/MS; fragments of soy anti-nutritional factors (Kunitz and Bowman-Birk trypsir, inhibitors), as well as of other soybean proteins, were identified, confirming that these proteins were hydrolyzed. The protein extracts at time 0 h and 8 h were analyzed by RP-HPLC; one fraction was analyzed by MS/MS, which identified peptides from Lactobacillus species. Determination of trypsin inhibitory activity showed less inhibition of the enzyme with inoculated soy flour compared to the control (un-inoculated soy flour), confirming the deactivation of trypsin inhibitors by fermentation. Determination of ACE inhibitory activity showed a higher inhibition with the control (86% +/- 3.0) compared to inoculated soy flour (66% +/- 7.6).

No description available.