Abstract Species of Lactobacillus (L.) are important starter and probiotic lactic acid bacteria used in the dairy industry. Industrial fermentation processes are prone to phage infections, which can cause severe economic losses. The main objective of this thesis was to examine in more depth the genetic variation and evolution of L. delbrueckii and L. rhamnosus phages. Aspects of interactions and co-evolution of a phage and its host have also been included in this study. In this study, the complete genomic DNA sequences of four Lactobacillus phages were determined and analyzed in detail. Specific phage genes and genetic elements were identified and studied in more depth. The L. delbrueckii phage JCL1032 was found to be a temperate phage which is able to integrate into two distinct genes of L. delbrueckii, but with exceptionally low frequency. The isolated JCL1032-lysogenic bacteria expressed a complex phage resistance against several L. delbrueckii phages. The rarely reported coexistence of phage adsorption resistance and immunity could not be explained by lysogenic conversion. Instead, the spontaneously induced JCL1032 may have provided a selective advantage to adsorption resistant lysogens. The biological activity of two group I introns residing within the terminase large subunit and tape measure genes of the JCL1032 genome (49,433 bp) was demonstrated. The diversification of L. delbrueckii phages is mainly due to insertions, deletions and recombination, as was demonstrated by comparative analyses of the LL-Ku and c5 genomes of 31,080 bp and 31,841 bp, respectively. Interestingly, both phages have possible autonomous transcription units of genes within their genomes. It seemed that evolution of the 36,366-bp genome of the L. casei phage Lc-Nu has been fuelled by deletions as well. The lytic phage Lc-Nu has an imperfect lysogeny module and the phage is genetically closely related to L. casei prophages. This clearly demonstrated that Lc-Nu has a recent temperate origin. This study provides genetic tools, genes, and regulatory elements for biotechnological applications and for developing starter strains with enhanced phage resistance properties. / Tiivistelmä Hapatteina ja probiootteina käytetyt Lactobacillus-maitohappobakteerit (L. ) ovat merkittävässä asemassa meijeriteollisuudessa. Teolliset käymisprosessit ovat alttiita faagi-infektioille, jotka voivat aiheuttaa tuotantolaitoksille huomattavia taloudellisia tappioita. Tämän tutkimuksen päätavoitteena oli syventää tietoa L. delbrueckii ja L. rhamnosus -bakteereita infektoivien faagien geneettisestä muuntelusta ja evoluutiosta. Tutkimuksessa käsitellään myös faagin ja isäntäbakteerin välistä vuorovaikutusta sekä yhteisevoluutiota. Tutkimuksessa määritettiin neljän Lactobacillus-faagin genominen DNA-sekvenssi, identifioitiin faagigeenejä ja muita geneettisiä elementtejä sekä tutkittiin niiden toimintaa. L. delbrueckiin JCL1032-faagi osoittautui tutkimuksessa temperaatiksi. JCL1032-genomi voi integroitua kahteen eri geeniin isäntäbakteerin kromosomissa, joskin lysogeniafrekvenssi on hyvin alhainen. Tutkimuksessa eristetyt JCL1032-lysogeeniset bakteerikannat olivat resistenttejä useille Lactobacillus-faageille. Osassa lysogeenisia bakteereita resistenssi ilmeni jo faagin adsorptiovaiheessa. Vastaavanlainen ilmiö on kuvattu vain harvoin aiemmin. Havaittua kompleksista resistenssiä ei voitu selittää lysogeenisella konversiolla. Sen sijaan ilmiön taustalla voi olla JCL1032-profaagien spontaani indusoituminen bakteerin kromosomista, mikä voi antaa valintaetua adsorptioresistenteille lysogeenisille bakteereille. JCL1032-genomissa (49 433 emäsparia) osoitettiin olevan kaksi biologisesti aktiivista intronia terminaasin suurta alayksikköa ja hännän mittaproteiinia koodaavissa geeneissä. LL Ku- ja c5-faagien genomien (31 080 ja 31 841 emäsparia) vertailu osoitti L. delbrueckii -faagien evoluution olevan pääasiassa seurausta insertioista, deleetioista ja rekombinaatiosta. Kummassakin genomissa oli mahdollisesti päällekkäisiä ja itsenäisesti transkriptoituvia geenialueita. Deleetiot ovat muokanneet myös L. casein lyyttisen Lc- Nu-faagin genomia (36 466 emäsparia). Faagin lysogeniamoduuli sisälsi vain osan lysogeeniseen elinkiertoon tarvittavista geeneistä. Lc-Nu on geneettisesti läheistä sukua L. casei -profaageille, mikä myös viittaa siihen, että Lc-Nu on kehittynyt temperaatista faagista. Tutkimustuloksia faagien geeneistä ja säätelyelementeistä voidaan hyödyntää hapatebakteerien faagiresistenssiominaisuuksien kehittämisessä sekä erilaisissa bioteknologisissa sovelluksissa.

Les amines biogènes sont des composés allergènes, notamment rencontrés dans les produits fermentés tel que le vin. Les bactéries lactiques du vin, dont Oenococcus oeni, le principal acteur de la fermentation malolactique, sont capables de produire ces molécules, à partir de précurseurs azotés. Afin de réduire la teneur en amines biogènes, il est nécessaire de comprendre le rôle de cette production, chez les souches impliquées dans la synthèse de ces métabolites. Le projet européen BiamFood FP7 (n°211441) a été mis en place pour répondre à cette problématique. Au cours de mon travail de thèse, des outils moléculaires ont été développés afin de muter de manière ciblée les gènes de O. oeni et d’exprimer des gènes d’intérêt. Ainsi, les clusters hdc de Lactobacillus hilgardii et odc de O. oeni, responsables respectivement de la synthèse de l’histamine et de la putrescine, ont été clonés dans le vecteur pGID052 et transférés dans la souche de laboratoire O. oeni ATCC BAA-1163, déficiente pour la production d’amines biogènes. Cette stratégie n’ayant pas donnée lieu à la production d’amine biogène, mon travail de recherche s’est orienté vers la caractérisation biochimique de l’ornithine décarboxylase de O. oeni. L’ornithine décarboxylase de O. oeni BR14/97 a été sur-produite chez E. coli via le système pET. Après purification de l’enzyme, le pH optimal et la température optimale de fonctionnement, 5,5 et 35°C respectivement, ont été caractérisés. Les constantes cinétiques Km = 1 mM et Vmax = 0,57 U. mg-1 ont également été déterminées en mesurant la putrescine produite par HPLC (Gomez-Alonso et al, 2007). De plus, l’ODC de O. oeni BR14/97 est spécifique de la L-ornithine et ne peut pas dégrader la L-lysine en cadavérine, ce qui implique la présence d’une voie métabolique propre à la production de cadavérine chez cette souche. Dans un second axe du projet, l’influence de la source azotée et notamment des peptides versus acides aminés libres, a été étudiée chez une souche de Lactobacillus plantarum, isolée du vin et productrice de tyramine. Les peptides contenant de la tyrosine, sont utilisés par cette souche pour former de la tyramine. La production augmente en phase stationnaire de croissance, et est corrélée à l’expression du transporteur tyrP. L’analyse de la tyrosine présente dans le milieu de culture montre que ces peptides seraient dégradés dans le milieu extracellulaire chez L. plantarum. / Biogenic amines are indesirable compounds found in fermented products like wine. Lactic acid bacteria from wine, including Oenococcus oeni, the main actor of malolactic fermentation, are able to produce these molecules from nitrogenous precursors. In order to limited biogenic amines accumulation, it is necessary to understand the role of this production by strains responsible for the synthesis of these metabolites in food. That is why the European BiamFood project was put in place. Along my thesis, molecular tools were developed in order to mutate O. oeni genes (encoding decarboxylases), and to express genes of interest. Genetic clusters hdc from L. higardii and odc from O. oeni, responsible for histamine and putrescine synthesis respectively, were cloned into the pGID052 vector and transferred into the laboratory strain O. oeni ATCC BAA-1163, which is not able to produce any biogenic amines. However no biogenic amines production was observed. My work thesis was then redirected in the in vitro biochemical characterization of the ODC from O. oeni. The odc from O. oeni BR14/97 was overproduced in E. coli BL21 via the pET system. Optima pH and temperature were determined with the purified enzyme obtained. Kinetic constants Km = 1 mM and Vmax = 0,57 U.mg-1 were also determined by measuring putrescine production by HPLC (Gomez-Alonso et al, 2007). Furthermore, ODC from O. oeni BR14/97 is specific for the L-ornithine and can not decarboxylated the L-lysine into cadaverine. In a second part of the BiamFood project, the impact of nitrogen sources, especially peptides compared to free amino acids, was studied in a Lactobacillus plantarum strain, isolated from wine and able to produce tyramine. Peptides containing tyrosine residues are used by this strain to produce tyramine. Tyramine production increases during the growth and reaches a maximum at stationary phase. The production is correlated with tyrP expression. The tyrosine measured in culture media shows that peptides may be hydrolyzed in the extracellular medium in L. plantarum.

Nous avons étudié la présence de bactéries lactiques capables de produire des bactériocines dans des fromages traditionnels Slovènes. Dans cinq échantillons de Tolminc (fromage au lait de vache) et quatre échantillons de Kraški ovčji sir (fromage au lait de brebis), nous avons recherché la présence de 19 gènes de bactériocines par PCR. L'ADN a été extrait directement à partir des fromages ainsi qu'à partir de consortia microbiens de ces fromages isolés sur gélose CATC, Rogosa et M17. Nous avons utilisé des tests par diffusion sur gélose pour déterminer l'activité antimicrobienne des consortia sur différentes bactéries indicatrices. L'activité anti-staphylococcique a aussi été déterminée in situ dans du lait et du fromage. L'avantage compétitif des souches productrices de bactériocines a été évalué en effectuant des repiquages successifs des consortia dans du lait. Lors de ces essais, nous avons suivi la présence de différents déterminants génétiques de bactériocines ainsi que l'activité antimicrobienne des consortia. Ces mêmes propriétés ont aussi été déterminées pour des souches individuelles productrices de bactériocines, qui ont été isolées du consortium initial ou de consortia obtenus après propagation dans le lait. La mise en évidence de gènes de bactériocines par PCR dépendait de l'efficacité d'extraction de l'ADN. L'extraction de l'ADN total était plus efficace lorsque l'homogénéisation du fromage était réalisée avec une solution de citrate de sodium. Dans l'ADN issu des fromages et consortia microbiens, nous avons détecté plusieurs gènes de bactériocines. Leur nombre diminuait lors de la propagation dans le lait, ce qui indique un faible avantage compétitif des souches productrices de bactériocines. Les résultats n'ont montré un avantage compétitif que pour des souches comportant des déterminants génétiques de la cytolysine. Nous n'avons détecté une production de bactériocines dans les fromages que lorsque qu'une culture pure d'une souche productrice de nisine A a été ajoutée. La différence entre la détection de déterminants génétiques de bactériocines et l'activité antimicrobienne montre la complexité qui relie ces deux propriétés.En raison des limitations concernant les tests par diffusion sur gélose pour détecter l'expression des gènes in situ, nous avons mis en place une méthode moléculaire basée sur la reverse transcription et la PCR en temps réel. Cette méthode sera très utile pour de futures études concernant le rôle des bactériocines dans les fromages. / We examined the presence of lactic acid bacteria (LAB) able to produce different bacteriocins in traditional Slovenian cheeses. In five samples of Tolminc cheese (from cows' milk) and four samples of Kraški ovčji sir (from ewes' milk) we looked for the presence 19 LAB bacteriocins' gene determinants using PCR. The DNA analysed was extracted directly from cheese samples as well as from cultivable microbial consortia of cheese which were isolated on CATC, Rogosa and M17 agar media. We used diffusion tests to determine the antimicrobial activity of microbial consortia against different indicator bacteria. Anti-staphylococcal activity was also determined in situ in milk and cheese. Competitive advantage of bacteriocinogenic strains was examined by consecutive propagation of microbial consortia in milk. During this we followed the presence of different bacteriocin gene determinants and antimicrobial activity of microbial consortia. The same properties were also determined for individual bacteriocinogenic strains that were isolated from initial consortia and from consortia obtained after propagation in milk. The success of finding bacteriocin gene determinants with PCR depended greatly on the efficiency of DNA extraction. The extraction of total DNA was the most successful when sodium citrate was used for cheese homogenisation. In DNA of different cheeses and microbial consortia we detected a number of bacteriocin gene determinants. Their number was reduced during the process of propagation in milk, which indicates a poor competitive advantage of some bacteriocinogenic strains. The results demonstrated competitive advantage only for strains that carried gene determinants for cytolysin. We detected bacteriocin activity in cheese only when monoculture of nisin A producer was added. The discrepancy between detected bacteriocin gene determinants and antimicrobial activity shows the complexity that links these two properties. This method will be very useful in the future studies of the role of bacteriocins in cheese.

Lactobacillus sakei est une bactérie lactique qui fait partie de la flore dominante de la viande. Elle possède un équipement génétique inhabituel chez les bactéries lactiques, dédié à l'utilisation du fer : des transporteurs et 3 régulateurs de transcription fer-dépendants de la famille Fur. Nous avons i) évalué la capacité de L. sakei à utiliser les sources de fer de son environnement en développant une méthode de microanalyse du fer par microscopie (EELS) et spectrométrie de masse (Nano-SIMS), ii) réalisé une étude fonctionnelle des 3 régulateurs Fur-like et iii) réalisé une analyse transcriptomique globale en présence de transferrine ou d'hème. Ce travail a montré que le fer sous forme complexé, transferrine ou hème, était internalisé et améliorait la survie de L. sakei. Nous avons montré que la catalase hème-dépendante n'est pas l'acteur principal de cette survie car un mutant ΔkatA survit comme la souche sauvage en présence d'hème. Nos travaux ont montré aussi que le fer et l'hème induisent des réponses globales différentes. L'hème a un effet protecteur alors que le fer induit plus de stress. Nous avons mis en évidence que les 3 régulateurs Fur-like sont fonctionnellement distincts. Le régulateur Mur est impliqué dans l'homéostasie du manganèse, le PerR régule des gènes impliqués dans la réponse au stress oxydant et le Fur est impliqué dans la séquestration du fer, la morphologie des cellules et la résistance au stress. Cette étude montre que le fer et l'hème conduisent à des réponses cellulaires différentes chez L. sakei et indique que ce métabolisme pourrait être un facteur important pour la compétitivité dans l'écosystème carné. / Lactobacillus sakei is a meat-borne lactic acid bacteria. This species harbors a quite complete genetic equipment dedicated to iron utilization such putative iron transporters and 3 transcriptional iron-dependent regulators of the Fur family. We evaluate L. sakei ability to use iron sources encountered in its natural environment by i) developing an iron microanalysis method coupling microscopy (EELS) and mass spectrometry (Nano-SIMS), ii) functional study of the 3 Fur-like regulators and iii) global transcriptomic analysis in response to transferrin or heme. This work shows that iron in complexed forms (transferrin or heme) is internalized and leads to an enhanced survival in L. sakei cells. We show that the heme-dependant catalase is not the main factor implicated in this survival phenotype as the ΔkatA strain is not affected in its survival when heme is provided. Our work has revealed that heme and iron lead to different global responses. It also indicates a protecting effect of heme whereas transferrin induces stress. We show that the 3 Fur-like regulators belong to three functional families. The Mur regulator is implicated in manganese homeostasis, the PerR regulates genes implicated in the oxidative stress response and the Fur is implicated in iron storage, cells morphology and stress resistance. This study proves that heme and iron lead to different cellular responses in L. sakei and indicates that this metabolism could be an important adaptative factor in meat ecosystem.

Listeria monocytogenes causa a listeriose, uma doença zoonótica grave que causa infecções do sistema nervoso central (meningite, encefalite e meningoencefalite), bacteremia primária e septicemia. A doença apresenta baixa morbidade e alta mortalidade e acomete, principalmente, grupos de risco, como mulheres grávidas, neonatos, indivíduos imunocomprometidos e idosos. L. monocytogenes tem sido encontrada com freqüência em alimentos in natura e/ou processados, como queijos e outros produtos lácteos. Esse estudo objetivou isolar bactérias lácticas a partir de leite de cabra, capazes de produzir peptídeos antimicrobianos (bacteriocinas), identificar estas cepas, caracterizar as bacteriocinas produzidas e avaliar o seu potencial de aplicação no controle da multiplicação de L. monocytogenes em queijo de cabra durante armazenamento a 8-10°C. Trabalhando-se com leite de cabra cru, foi possível isolar seis cepas produtoras de bacteriocinas (DF2Mi, DF3Mi, DF4Mi, DF5Mi, DF6Mi e DF60Mi). Através de testes fenotípicos apropriados e sequenciamento do 16S rRNA, essas cepas foram identificadas como Lactococcus lactis subsp. lactis (DF2Mi, DF3Mi, DF4Mi e DF5Mi), Leuconostoc lactis (DF6Mi) e Lactobacillus paracasei subsp. paracasei (DF60Mi). A caracterização físico-química e biológica das bacteriocinas produzidas pelas cepas DF4Mi, DF6Mi e DF60Mi indicou que eram resistentes ao calor e extremos de pH, mas apresentavam características diferentes em relação ao espectro de ação, sensibilidade a agentes químicos, adsorção à células-alvo e lise das células de L. monocytogenes. O efeito do pH, temperatura e composição do meio de cultura na produção das bacteriocinas foi também cepa-dependente. A cepa DF4Mi apresentou melhor atividade antimicrobiana e foi selecionada para o estudo de inibição de L. monocytogenes em queijos. Para isso, foram preparados lotes de queijo frescal, feito com leite de cabra pasteurizado adicionado e não adicionado da cepa DF4Mi (106 UFC/mL), experimentalmente contaminado com L. monocytogenes (103 UFC/g), além dos controles positivo (queijo adicionado de nisina 12,5 mg/Kg) e negativo (leite adicionado de uma cepa de L. lactis subsp. lactis não bacteriocinogênica). Observou-se que a cepa DF4Mi apresentou efeito bacteriostático no queijo, sendo capaz de inibir a multiplicação do patógeno durante o armazenamento a 8-10°C por 10 dias. No entanto, inibição semelhante foi obtida nos queijos com a bactéria lática não bacteriocinogênica, indicando que a inibição não pode ser creditada às bacteriocinas. Nos queijos-controle com nisina, foi observada uma redução de 2 log na contagem de L. monocytogenes após 10 dias a 8-10°C. Já nos queijos preparados sem nisina e sem nenhuma bactéria lática, as contagens de L. monocytogenes atingiram contagens elevadas (106 UFC/g) após 10 dias de armazenamento a 8-10°C. / Listeria monocytogenes causes listeriosis, a serious zoonotic disease that causes infections in the central nervous system (meningitis, encephalitis and meningoencephalitis), bacteremia and septicemia. The disease presents low morbidity and high mortality and affects mainly those in the risk group, such as pregnant women, neonates, immunocompromised individuals and the elderly. L. monocytogenes has been frequently detected in in natura and processed foods. Like cheeses and other dairy products. This study aimed to isolate lactic acid bacteria capable of producing antimicrobial compounds from goat milk, identify the isolates, characterize the bacteriocins and evaluate their potential application in controlling the growth of L. monocytogenes in goat cheese during storage at 8-10°C. Six bacteriocinogenic strains (DF2Mi, DF3Mi, DF4Mi, DF5Mi, DF6Mi e DF60Mi) were successfully isolated from raw goat milk. Using appropriate phenotypic tests and 16S rRNA sequencing, these strains were identified as Lactococcus lactis subsp. lactis (DF2Mi, DF3Mi, DF4Mi e DF5Mi), Leuconostoc lactis (DF6Mi) and Lactobacillus paracasei subsp. paracasei (DF60Mi). The physico-chemical and biological characterization of the bacteriocins produced by the strains DF4Mi, DF6Mi e DF60Mi indicated that they were resistant to heat and pH extremes, but presented different spectrum of activity, sensitivity to chemicals, adsorption to target cells and lysis of L. monocytogenes. The effect of pH, temperature and culture media composition in bacteriocin production was also strain-dependent. The strain DF4Mi presented the best antimicrobial activity and was selected for the studies on inhibition of L. monocytogenes in cheese. Frescal cheese was manufactured with pasteurized goat milk added of a culture of DF4Mi (106 CFU/mL), and experimentally contaminated with L. monocytogenes (103 CFU/g). Control cheeses were also prepared: those added of 12.5 mg/Kg nisin (positive control) and those added of a non-bacteriocinogenic L. lactis subsp. lactis strain. The strain presented a bacteriostatic effect, controlling the growth of the pathogen for 10 days at 8-10°C. However, a similar effect was observed in the cheeses prepared with the non-bacteriocinogenic strain, indicating that the inhibition cannot be credited to bacteriocins. In the cheeses containing nisin, a 2 log reduction in the counts of L. monocytogenes was achieved after 10 days at 8-10°C. In the cheeses with no added nisin or lactic acid bacteria, the counts of L. monocytogenes after 10 days at 8-10°C were high (106 CFU/g).

Após a constatação da escassez de estudos realizados com vegetais crus na busca por novas estirpes de bactérias láticas (BAL) produtoras de bacteriocinas e diante do potencial tecnológico da aplicação destas cepas tanto como agentes de conservação em alimento, bem como cultura probiótica em alimentos funcionais, este estudo objetivou isolar e identificar cepas de bactérias láticas potencialmente bacteriocinogênicas de amostras de rúcula obtidas no comércio local de São Paulo, SP - Brasil, identificar e caracterizar as bacteriocinas produzidas pelos isolados e avaliar o potencial probiótico dos isolados testando sua sobrevivência no modelo dinâmico do trato gastrointestinal TNO gastro-Intestinal Model - TIM-1 disponível no TNO (The Netherlands Organization for Applied Scientific Research) divisão Quality of Life (Zeist, Holanda). A produção de bacteriocinas neste modelo também foi avaliada, comparando-se com L. sakei 2a, também produtora de bacteriocinas e ainda avaliou-se a interferência na viabilidade de E. faecium LMA1. A cepa Lactococcus lactis subsp. lactis MK02R de rúcula produziu uma bacteriocina sensível à enzimas proteolíticas, termoestável e não influenciada pelo pH, sendo capaz de inibir Enterococcus faecium, Lactobacillus sakei, Listeria innocua, Lactobacillus delbrueckii e Listeria Monocytogenes de diferentes grupos sorológicos. Os ensaios genéticos utilizando primers Nisf e Nisr confirmaram que a bacteriocina MK02R é uma nisina, apresentando uma alteração dos aminoácidos no peptídeo líder em relação às nisinas A, Z, Q, F e U, porém com a estrutura do peptídeo maduro idêntica ao da nisina F. Estes resultados foram confirmados por espectrometria de massas de amostras purificadas por HPLC. L. lactis MK02R resistiu à passagem no modelo dinâmico TIM-1, apresentando uma alta capacidade de sobreviver nas condições simuladas do trato gastrointestinal humano. Entretanto, não foi capaz de causar a redução no número de E. faecium LMA1. Em contrapartida, L. sakei 2a, mesmo apresentando uma sobrevivência menor, foi capaz de causar uma redução de 70% na população de E. faecium LMA1 no ambiente simulado do TGI. Não foi detectada atividade residual da ação antimicrobiana das bacteriocinas produzidas por L. lactis MK02R ou L. sakei 2a após a passagem pelo modelo dinâmico TIM-1. Estes resultados evidenciam a possível aplicação de L. lactis MK02R como um agente de controle biológico na conservação de alimentos e também como uma cultura potencialmente probiótica. / Given the scarcity of studies performed with raw vegetables addressing the search for new bacteriocinogenic strains of lactic acid bacteria (LAB) and considering the technological application of these strains as food preservatives and probiotic cultures in functional foods, this study was aimed at isolation and identification of bacteriocinogenic LAB strains from samples of rocket salad obtained in the local market of São Paulo, SP - Brazil, subsequent characterization of the bacteriocins produced by these LABs and evaluation of their probiotic potential by testing their survival in the dynamic gastrointestinal model TNO gastro- Intestinal-Model - TIM-1, available at the TNO (Netherlands Organization for Applied Scientific Research) Quality of Life division (Zeist, Netherlands). The studies in the TIM-1 model were also done with another bacteriocinogenic strain L. sakei 2a for comparison, evaluating their interference on the viability of E. faecium LMA1. The bacteriocin produced by strain Lactococcus lactis subsp. lactis MK02R isolated from rocket salad was sensitive to proteolytic enzymes, heat-stable and not influenced by the pH. The bacteriocin inhibited the growth of Enterococcus faecium, Lactobacillus sakei, Listeria innocua, Lactobacillus delbrueckii the primers Nisf and Nisr indicated that the bacteriocin produced by the strain MK02R is a nisin, with a change in the amino acid sequence of the leader peptide when compared to nisin A, Z, Q, U and F, but with the structure of the mature peptide homologous to that of nisin F. These results were confirmed by mass spectrometry of purified samples obtained by HPLC. L. lactis MK02R withstood the test in the dynamic model TIM-1, presenting capability to survive in the simulated conditions of the human gastrointestinal tract. However, the strain was not able to cause a reduction in the number of E. faecium LMA1. On the other hand, L. sakei 2a, even presenting lower survival, was able to cause 70% reduction in the population of E. faecium LMA1 in the gut simulated environment. No residual antimicrobial activity of bacteriocin produced by L. lactis MK02R or L. sakei 2a was detected after the transit through the dynamic model TIM-1. These results demonstrate the possible application of L. lactis MK02R both as a biocontrol agent in food preservation and as a potentially probiotic culture.

Les maladies inflammatoires chroniques de l’intestin (MICI) regroupent la colite ulcéreuse (CU) et la maladie de Crohn (MD) qui sont des troubles intestinaux caractérisés par une inflammation chronique du tractus gastro-intestinal. Les MICI sont provoquées par un dysfonctionnement du système immunitaire de la muqueuse vers le microbiote intestinal chez les individus génétiquement prédisposés, menant à des réponses immunitaires pro-inflammatoires excessives. L'incidence de ces maladies augmente dans les pays développés et sont devenues de grands problèmes gastroentérologiques, surtout que les médicaments de traitement actuels sont associés à de graves effets collatéraux. Ainsi, les dernières recherches se concentrent sur le développement de nouvelles stratégies pour le traitement des MICI. Les probiotiques, en particulier celles qui appartiennent au groupe des bactéries lactiques (BL), se montrent capables de prévenir et de traiter les MICI en rétablissant l'équilibre du microbiote perturbé et en supprimant les réponses immunitaires pro-inflammatoires. Afin d'augmenter l’effet probiotique des BL, le clonage moléculaire et l'expression des molécules anti-inflammatoires ont été réalisés et les souches recombinantes des BL ont été évaluées comme un traitement alternatif pour les MICI. L'utilisation de ces souches, en particulier le modèle Lactococcus lactis, a montré son efficacité dans la lutte contre l'inflammation intestinale. Son administration comme thérapie pour traiter d'autres maladies inflammatoires du tractus gastro-intestinal, tels que la mucite, a également été évaluée. La mucite est un effet secondaire fréquent chez les patients subissant une radiothérapie ou une chimiothérapie qui affecte fortement leur qualité de vie. Comme pour les MICI, le traitement de la mucite est assez limité, seuls quelques médicaments et procédures décrits peuvent en effet contenir les ulcérations et l'inflammation. Par conséquent, ilest nécessaire de développer des traitementsalternatifs pour les MICI et la mucite. Le but de cette étude est de tester l'efficacité de la souche de L. lactis recombinante exprimant la protéine associée à la pancréatite I (PAP) afin de lutter contre les MICI et la mucite dans des modèles de souris. La PAP a été rapportée comme une protéine ayant des propriétés antimicrobiennes qui jouent un rôle important pour maintenir l'homéostasie intestinale. Tout d'abord, nous avons construit et confirmé l'expression de la PAP humaine par recombinant L. lactis. Ensuite, nous avons évalué l'effet thérapeutique de cette souche dans un modèle de souris de Dinitrobenzene acide sulfonique (DNBS) afin d’induire la colite. En outre, la livraison de PAP par lactocoques a protégé les animaux d’une perte de poids, de la perméabilité intestinale, et de lésions tissulaires. De plus, le traitement L. Lactis-PAP a diminué Th1 (IFN-y), Th2 (IL-4, IL-5) et Th17 (IL-17) de type-réponses immunitaires. On a également observé une expression élevée de régulation de cytokines TGF-β ainsi qu’une augmentation de la quantité de cellules T régulatrices chez les souris traitées. Les effets anti-inflammatoires des L. Lactis-PAP et des souches des produits laitiers L. lactis NZ9000 ont également été mesurés dans le modèle d'inflammation des muqueuses 5-Fluorouracil (5-FU). L'administration de L. lactis NZ9000 hébergeant le vecteur pSEC sans l'ADNc de PAP a été en mesure de prévenir les dommages histologiques, de réduire l’infiltration des éosinophiles et de la sécrétion d'IgA dans l'iléon de souris. D'autre part, L. lactis exprimant la PAP a conservé l'architecture muqueuse et a amélioré l'activité des cellules de Paneth. En même temps, nos résultats démontrent que L. lactis, exprimant PAP est une stratégie prometteuse pour traiter les MICI. En outre, la souche L. lactis NZ9000 de manière surprenante, a présenté des effets anti-inflammatoires chez les souris injectées avec du 5-FU. / Inflammatory Bowel Diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD) are complex intestinal disorders characterized by chronic inflammation of the gastrointestinal tract (GIT). IBD are caused by a deregulation of the mucosal immune system toward the native intestinal microbiota in genetically predisposed individuals, leading to excessive pro-inflammatory immune responses in the GIT. The incidence of both diseases is increasing in developed countries turning CD and UC a main gastroenterological problem as current treatment drugs are associated with serious side effects. Thus, recent research is focusing on the development of new strategies for the treatment of IBD. Probiotic bacteria especially the ones belonging to the lactic acid bacteria (LAB) group, were shown to be capable of preventing and treating IBD by restoring the balance of disrupted microbiota and suppressing pro-inflammatory immune responses. In order to increase LAB probiotic effect, molecular cloning and expression of anti-inflammatory molecules are being carried out and LAB recombinant strains are also being evaluated as an alternative treatment for IBD. As the use of these strains, especially the model Lactococcus lactis, showed to be very effective in fighting intestinal inflammation, its administration as a therapy for treating other human GIT inflammatory diseases, such as mucositis, are also being evaluated. This disorder is a common side effect of patients undergoing radiotherapy or chemotherapy that strongly affects their quality of life. Like IBD, treatment for mucositis is very limited with few medicaments and procedures described to contain inflammation. Therefore, given the need to develop alternative treatments for both IBD and mucositis, this study aimed to test theefficacy of either dairy L. lactis NZ9000 or recombinant L. lactis strain expressing Pancreatitis Associated Protein I (PAP) to fight inflammation in mouse models of IBD and mucositis. PAP has been reported as a protein with antimicrobial properties that plays important roles to keep intestinal homeostasis. Firstly, we constructed and confirmed the expression of human PAP by recombinant L. Lactis. Afterwards, we evaluated the therapeutic effect of this strain in a mice model of dinitrobenzenosulfonic acid (DNBS)-induced colitis. Moreover, PAP delivery by lactococci protected animals from weight loss, intestinal permeability, and tissue damage. In addition, L. lactis-PAP treatment decreased Th1 (IFNγ), Th2 (IL-4, IL-5) and Th17 (IL-17) type-immune responses. It was also observed a higher expression of regulatory TGF-β cytokine and increased amount of T regulatory cells in treated mice. The anti-inflammatory effects of both L. lactis-PAP and dairy L. lactis NZ9000 strains were also measured in 5-fluoracil mucositis model. We showed that this model was successfully reproduced in BALB/c mice with an induction of acute inflammation in the small bowel of animals. Administration of L. lactis NZ9000 harboring pSEC vector without the cDNA of PAP was able to prevent histological damage, reduce eosinophils infiltrate and IgA secretion in the ileum of mice. On the other hand, L. lactis expressing PAP preserved mucosal architecture and improved Paneth cells activity. Taking together, our results demonstrate that L. lactis, expressing PAP peptide is a promising strategy to treat IBD. Moreover, L. lactis NZ9000 strain, derived from dairy L. lactis MG1363, surprisingly presented anti-inflammatory effects in mice injected with 5-FU.

Zvýšená konzumace fermentovaných mléčných výrobků v posledních letech vede k zavádění nových výrobků na trh. Funkční a probiotické produkty jsou v dnešní době také hojně rozšířeny. Cílem diplomové práce bylo posoudit mikrobiální kvalitu komerčních jogurtů a nefarmakologických probiotických výrobků. Bylo zkoumáno 24 vzorků jogurtů a 8 vzorků probiotických mléčných výrobků. Pozornornost byla zaměřena zvláště na kvantifikaci mikroorganismů v jednotlivých výrobcích a na sledování viability buněk. Většina mléčných produktů obsahovala počty odpovídající minimální požadované hodnotě 1x107cfu/ml. Nicméně byly objeveny produkty, které neobsahovaly živé bakterie nebo obsahovaly jen jejich menší množství. To platí zejména pro běžné jogurty. Probiotické mléčné výrobky v zásadě obsahovaly větší množství bakterií než jogurty, protože je u nich navíc požadováno 1x106cfu/ml minimálního množství specifických bakterií jiných než jogurtových startovacích kultur. Isoláty z fermentovaných mléčných výrobků byly identifikovány jako Streptococcus thermophilus and Lactobacillus spp. Isoláty byly poté rozlišeny na jednotlivé kmeny pomocí RAPD použitím tří různých primerů. Byla zjištěna velká různorodost mezi kmeny rodu Lactobacillus spp. používaných různými podniky.

The aim of this study was focused on the study of conditions of growth of strains Lbc. paracasei subsp. paracasei CCDM 211, Lbc. paracasei CCDM 212, Lbc. paracasei subsp. paracasei CCDM 213 and Lbc. salivarius CCDM 216 in media with different amount of carbon-source (glucose, lactose and whey). Next part of the experiment was dealed with study of conditions of bacteria growth at stress conditions (lower pH). The purity od bacterial culture was verified with help of streaking. Purity DNA isolated from bacteria was tested using agarose gel electrophoresis, DNA concentration was estimated spectrophotometricaly. The presence of bacteria of genus Lactobacillus was proved using polymerase chain reaction (PCR) with genus specific primers.

In this work the functionalised magnetic particles were tested with streptavidin to selective DNA isolation. The method of selective DNA isolation was tested by using DNA probiotic strain Lactobacillus paracasei subsp. paracasei CCDM 211/06. A test was done on the biotinyl oligonucleotic particles, which was immobilised by containing streptavidin and it was used like a DNA probe for isolation complementary DNA chain by means of DNA/DNA hybridization. The primer R 5´ bio and the biotinyl denatured specific PCR product were tested for species Lb. paracasei as a DNA probe. These following experimental conditions were optimized for selective DNA isolation: temperature and time of hybridization, amount of DNA and the release of DNA from microspheres. Isolation of DNA was verified by PCR with specific generic primers. The specific generic PCR product was amplified in extent 250 bp, which was detected by using electrophoresis in agarose gel. This optimized method was successfully used in selective isolation of DNA Lactobacillus from a complementary sample of supplementary food (BIFI pangamin).