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Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The grape and wine ecosystem contains fungi, bacteria and yeasts whose interactions contribute to the final wine product. While the non-Saccharomyces yeasts are dominant in the early stage of alcoholic fermentation, the later stage is always dominated by Saccharomyces cerevisiae. Although their presence in wine fermentation is often short-lived, the non-Saccharomyces yeasts are known to produce an array of extracellular hydrolytic enzymes which facilitate the extraction and release of aroma compounds, but might also play a role in microbial interactions. The present study aimed to investigate the microbial diversity of grape juice and to evaluate the potential of non-Saccharomyces yeasts to produce hydrolytic enzymes and display anti-fungal properties. To capture the microbial diversity, culture-dependent (plating) and –independent (Automated Ribosomal Intergenic Spacer Analysis (ARISA)) techniques were used in parallel. The fungal and bacterial ARISA displayed a wider range of operational taxonomic units (OTUs) in comparison to cultivation-based technique, demonstrating that ARISA is a powerful culture-independent technique applicable to ecological studies in wine. Some of the uncommon yeast isolates derived from our cultivation-based study were subjected to an enzymatic screening process. Hydrolases, such as chitinases, β-1,4-cellulases, β-1,3-1,6-glucanases, β-glucosidases, pectinases and acid proteases were specifically sought. Most of the yeast isolates exhibited chitinase, β-1,4-cellulase as well as β-1,3-1,6-glucanase activities. Only Metschnikowia chrysoperlae exhibited β-glucosidase activity. We also retrieved the partial chitinase gene sequences from M. chrysoperlae, Pichia burtonii, Hyphopichia pseudoburtonii that exhibited chitinase activity. Among the isolates, Pseudozyma fusiformata exhibited a strong antagonistic activity against the wine spoilage yeasts B. bruxellensis AWRI 1499 and B. anomalus IWBT Y105. Furthermore, we showed that the killer phenotype of P. fusiformata cannot be attributed to a viral encoded dsRNA. Finally, two metagenomic approaches were employed in an attempt to explore the indigenous microbiome in a more holistic manner, where we adopted whole metagenome Roche GS-FLX 454-pyrosequencing and construction of a fosmid library. The whole metagenome sequencing revealed a wide range of hydrolytic enzymes that showed homology to enzymes from different fungal and non-Saccharomyces yeast species. Moreover, the metagenomic library screening resulted in the retrieval of 22 chitinase and 11 β-glucosidase positive fosmid clones originating from yeasts. Two clones of interest, BgluFos-G10 and ChiFos-C21, were subjected to next generation sequencing. BgluFos-G10 revealed 2 ORFs exhibiting homology to glycosyl hydrolase family 16 proteins whereas no ORFs encoding chitinase enzymes could be identified in the ChiFos-C21 clone. However, all the potential ORFs identified exhibited homology to a gene cluster from Clavispora lusitaniae ATCC 42720, suggesting that the cloned DNA fragments belonged to a yeast species closely related to C. lusitaniae or members of the family Metschnikowiaceae. Overall, our study identified a variety of novel hydrolytic enzymes. However, retrieving the full gene sequences of these identified enzymes would be the immediate follow-up of our study. Moreover, the hydrolytic and antifungal activities exhibited by the yeast isolate could be of major interest in evaluating their potential as biocontrol agents against grapevine fungal pathogens and subsequently the wine spoilage yeasts. It would be interesting to evaluate as well the potential impact of these enzymes under wine making condition and could be our next step of investigation. / AFRIKAANSE OPSOMMING: Die druif en wyn ekosisteme bevat swamme, bakterië en giste en die interaksies van hierdie organismes dra by tot die finale wyn produk. Die nie-Saccharomyces giste is dominant in die vroeë stadium van die alkoholiese fermentasie, maar die latere fase word altyd gedomineer deur Saccharomyces cerevisiae. Alhoewel hulle teenwoordigheid in wyngistings gewoonlik kortstondig is, is die nie-Saccharomyces giste bekend vir die produksie van ‘n verskeidenheid ekstrasellulêre hidrolitiese ensieme wat die ekstraksie en vrylating van aroma komponente fasiliteer, en ook moontlik ‘n rol kan speel in mikrobiese interaksie. Hierdie studie beoog om die mikrobiese diversiteit van druiwesap te bestudeer en die potensiaal van nie-Saccharomyces giste te evalueer ten opsigte van die produksie van hidrolitiese ensieme, asook die demonstrasie van anti-swam eienskappe. Kweking-afhanklike (uitplating), asook –onafhanklike (Automatiese Ribosomale Intergeniese Spasieerder Analise (ARISA)) tegnieke is in parallel gebruik om die mikrobiese diversiteit te bepaal. Die swam en bakteriële ARISA het ‘n groter verskeidenheid van operasionele taksinomiese eenhede (OTUe) vertoon in vergelyking met die kweking-gebasseerde tegniek en dit demonstreer dat ARISA ‘n kragtige kweking-onafhanklike tegniek is, wat toepasbaar is in ekologiese studies van wyn . Sommige van die skaarser gisisolate, uit ons kweking -gebasseerde studie was vir ensiemaktiwiteite geskandeer. Daar is spesifiek gesoek vir hidrolases soos chitinases,β-1,4-sellulases, β-1,3-1,6-glukunases, β-glukosidases, pektinases en suur proteases. Die meeste gisisolate het chitinase,β-1,4-sellulase asook β-1,3-1,6-glukunase aktiwiteit vertoon. Slegs Metschinikowia chrysoperlae het β-glukosidase aktiwiteit vertoon. Ons het verder die gedeeltelike chitinase geensekwensies van M. chrysoperlae, Pichia burtonii en Hyphopichia pseudoburtonii wat chitinase aktiwiteit vertoon het, bepaal. Een isolaat, Pseudozyma fusiformata, het ‘n sterk antagonistiese aktiwiteit teenoor die wyn bederfgiste, Bretanomyces bruxellensis AWRI 1499 en B. anomalus IWBT Y105 vertoon. Verder het ons gewys dat die killer fenotipe van P. fusiformata nie gekoppel kan word aan’n viraal gekodeerde dsRNA nie. Ten laaste is twee metagenomiese benaderings, naamlik die volledige metagenoom Roche GS-FLX 454-pirovolgordebepaling en konstruksie van ‘n fosmied biblioteek, gebruik om die inheemse mikrobioom op ‘n meer holistiese wyse te bestudeer. Die volgordebepaling van die volledige metagenoom het ‘n wye verskeidenheid hidrolitiese ensieme aan die lig gebring wat homologie met ensieme van verskillende swamme en nie-Saccharomyces gisspesies getoon het. Verder het die skandering van die metagenomiese biblioteek die isolasie van fosmiedklone van gisoorsprong wat positief is vir chitinase aktiwiteit (22 klone) en β-glukosidase aktiwiteit (11 klone) tot gevolg gehad. Twee van hierdie klone, BgluFos-G10 en ChiFos-C21, is met volgende generasie volgordebepaling ontleed. BgluFos-G10 het twee oopleesrame (OLRe) wat homologie met glikosiel hidrolase familie 16 proteïene het, vertoon maar geen OLRe wat chitinase ensieme enkodeer kon in die ChiFos-C21 kloon geïdentifiseer word nie. Al die potensiële OLRe wat geïdentifiseer is, het homologie aan ‘n genepoel van Clavispora lusitaniae ATCC 42720 vertoon, wat daarop dui dat die gekloneerde DNS fragmente aan ‘n gisspesie behoort wat naverwant aan C. lusitaniae of lede van die Metschinikowiaceae familie is. In geheel gesien het ons studie ‘n verskeidenheid van nuwe hidrolitiese ensieme geïdentifiseer. Die bepaling van die volledige geenvolgordes van hierdie geïdentifiseerde ensieme sal die onmiddelike opvolg aksie van hierdie studie wees. Verder is die hidrolitiese en anti-swam aktiwiteite wat deur die gisisolate gedemonstreer is, van hoof belang, asook die evaluering van hulle potensiaal as biokontrole agente teen wingerd swampatogene en wyn bederfgiste. Dit sal ook interessant wees om die potensiële impak van hierdie ensieme onder wynmaakkondisies te bepaal, en dit kan dus ons volgende ondersoek stap wees.

This dissertation is focused on exploring the potential of bacteria for the biosynthesis of natural products with the purposes of generating novel natural product derivatives and of improving the titer of pharmaceutically important natural products. A wide variety of compounds from various sources have been historically used in the treatment and prevention of diseases. Natural products as a major source of new drugs are extensively explored due to their huge structural diversity and promising biological activities such as antimicrobial, anticancer, antifungal, antiviral and antioxidant properties. For instance, penicillin as an early-discovered antimicrobial agent has saved millions of lives, indicating the historical importance of natural products. However, the alarming rise in the prevalence of drug resistance is a serious threat to public health and it has coincided with the decreasing supply of new antibiotics. Bacteria with a tremendous undiscovered potential have still been one of the richest sources of bioactive compounds to tackle the growing threat of antibiotic-resistant pathogens. Nevertheless, the production level of those important compounds is often quite low, and often undetectable using current analytical techniques. To expand the chemical repertoire of nature and to increase the titer of the natural products, researchers have developed various strategies, such as heterologous expression, co-cultivation of different bacteria, optimization of fermentation conditions, discovery of new species, engineering of biosynthetic enzymes, and manipulating regulatory elements. Thus, in my dissertation research, I have exploited a few of these strategies. First, I heterologously expressed some of the biosynthetic genes from the sch biosynthetic gene cluster, resulted in the production of a novel glycosylated angucycline. I was also able to generate another new glycosylated derivative of angucycline through gene disruption of tailoring enzymes. In this research, I isolated two novel angucycline derivatives and gained new insights into the glycosylation steps in the biosynthesis of Sch47554 and Sch47555. Next, I engineered the regulatory elements in Streptomyces sp. SCC-2136 through the overexpression and targeted gene disruption approaches for enhanced production of pharmaceutically important angucyclines. The highest titer of Sch47554 was achieved in Streptomyces sp. SCC-2136/ΔschA4 (27.94 mg/L), which is significantly higher than the wild type. This work thus provides an initial understanding of functional roles of regulatory elements in the biosynthesis of Sch47554 and Sch47555 and several engineered strains with enhanced production of Sch47554. Last, I isolated a carotenoid-producing endophytic bacterium from the leaves of the yew tree and optimized the fermentation conditions for an improved yield of zeaxanthin diglucoside up to 206 ± 6 mg/L. With the introduction of an additional copy of the Pscrt gene cluster through an expression plasmid, the engineered strain Pseudomonas sp. 102515/pOKF192 produced zeaxanthin diglucoside at 380 ± 12 mg/L, which is 85% higher than the parent strain. This strain holds a great potential for the production of pharmaceutically important antioxidant agent, zeaxanthin diglucoside.

Les moisissures sont responsables de contaminations sur les produits de BVP et induisent des pertes économiques conséquentes. Dans ce contexte, les cultures bioprotectrices représentent un intérêt croissant comme alternative aux conservateurs chimiques. L’objectif de la première partie de cette étude a été d’évaluer in vitro et in situ l’activité antifongique de bactéries lactiques et propioniques contre cinq moisissures contaminants isolées de produits de BVP. Les bactéries les plus actives pendant les tests in vitro ont été testées in situ par pulvérisation de surface. Sur le milieu WFH, les isolats bactériens les plus actifs correspondent aux espèces Lactobacillus plantarum, reuteri et au groupe buchneri. Les souches plus actives après ces tests ont été testées par inclusion dans la recette du pain au lait et différentes souches ont montré un effet retard en particulier la souche Leuconostoccitreum qui semble retarder la croissance de Penicillium corylophilum après 10 jours. Dans la deuxième partie de cette étude, les surnageants de cultures actifs sont analysés pour identifier les composés antifongiques grâce à différentes traitements et différentes méthode telle que l’HPLC et la spectrométrie de masse. Les résultats suggèrent que les acides organiques jouent un rôle prépondérant dans l’activité antifongique et ont montré que les composés antifongiques retrouvés correspondaient aux acides lactique, acétique et propionique, à l’éthanol et au peroxyde d’hydrogène, ainsi que d’autres composés mais à plus faible échelle. Sur ces résultats, différentes combinaisons des composés identifiés ont été testées pour leur effet sur la germination et la croissance radiale de P. corylophilum et E. repens. Certaines de ces combinaisons ont montré les mêmes effets que le surnageant actif ce qui confirme l’implication des molécules identifiées dans l’activité. Les résultats suggèrent que l’acide acétique est responsable de la totalité de l’activité antifongique observée sur P. corylophilum et qu’il joue un rôle important dans l’inhibition de E. repens. La souche bactérienne sélectionnée pourrait représenter une possibilité de culture bioprotectrice pour les produits de BVP. / Molds are responsible for the spoilage of bakery products and thus, cause substantial economic losses. In this context, bioprotective cultures represent a growing interest as an alternative to chemical preservatives. The aims of the first part of this study was to evaluate the in vitro and in situ antifungal activity of lactic acid bacteria (LAB) and propionibacteria against five moulds species isolated from bakery products. The most inhibitorybacteria found during the in vitro test were evaluated in situ after surface spraying. In WFH medium, the most active LAB isolates belonged to the Lactobacillus plantarum, reuteri and buchneri groups. The most active strains were added directly during “pains au lait” preparation and differents strains present delayed effect in particular a strain of Leuconostoc citreum which seems to delay the growth of Penicillium corylophilum after 10 days. In the second part, supernatants were analyzed to identified and quantified antifungal compounds by different treatments and different methods like HPLC, mass spectrometry. The results suggested that organic acids played the most important role in the antifungal activity and show that the main antifungal compounds corresponded to lactic, acetic and propionic acids, ethanol and hydrogen peroxide, as well as other compounds present at low levels. Based on these results, various combinations of the identified compounds were used to evaluate their effect on spore germination and fungal growth of P. corylophilum and E. repens. Some combinations presented the same activity than the bacterial culture supernatant thus confirming the involvement of the molecules in the antifungal activity. The results suggested that acetic acid was responsible of the entire antifungal activity against Penicillium corylophilum and played an important role in Eurotium repens inhibition. The selected bacteria provide a future prospect for use as bioprotective cultures on bakery products.

Coral diseases have become more prevalent and destructive over the past 20 years, possibly due to an increase in stressful environmental factors that may weaken corals defenses against disease. Aspergillosis is a disease caused by the fungus Aspergillus sydowii, which apparently infects only two species of gorgonian corals in the Caribbean Ocean (Gorgonia ventalina and G. flabellum). We hypothesized that the differential resistance to infection is caused by differences in chemical defenses among gorgonians. Freeze-dried gorgonian powders and extracts deterred fungal growth, but potencies varied among gorgonian species and among fungi. Extracts and powders generated from G. ventalina all strongly inhibited fungal growth. Since G. ventalina was predicted to have weak antifungal chemical defenses compared to gorgonians not known to suffer from aspergillosis, we concluded that gorgonian susceptibility to fungal infection is determined by factors other than, or in addition to, chemical defenses. In order to investigate specific gorgonian antifungal strategies, we attempted to use bioassay-guided fractionation to isolate antifungal compounds from four gorgonians: Gorgonia ventalina, Briareum asbestinum, Eunicea succinea, and Pseudopterogorgia americana. We succeeded in isolating two antifungal compounds, diastereomers of 9,11-seco-24-hydroxydinosterol, from the gorgonian Pseudopterogorgia americana. This compound was previously identified by other groups, but this study is the first to establish its antifungal activity. At natural concentration, one diastereomer of 9,11-seco-24-hydroxydinosterol inhibited the growth of three different fungi, suggesting that at least this diastereomer may possess broad-spectrum antifungal activity. The results from our survey of gorgonian chemical defenses indicate that susceptibility to aspergillosis cannot be explained by chemical growth inhibition alone. Further areas of investigation include induction of gorgonian chemical defenses, examination of growth-inhibiting mechanisms of antifungal metabolites, and identification of non-chemical factors affecting gorgonians vulnerability to fungal infection.

Orientador: Marcia Regina Braga / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-12T18:52:46Z (GMT). No. of bitstreams: 1 Simoes_Kelly_D.pdf: 3512548 bytes, checksum: 21ccb89a97ae81d965d0171998569c9e (MD5) Previous issue date: 2008 / Resumo: Sesbania virgata (Cav.) Pers. e Hymenaea courbaril L. var. stilbocarpa (Fabaceae) são duas espécies tropicais que acumulam, respectivamente, galactomanano e xiloglucano como polissacarídeos de reserva nas sementes, os quais são mobilizados logo após protrusão da radícula, gerando grande quantidade de monossacarídeos e oligossacarídeos. Parte desses açúcares é liberada para o meio, sem que haja, contudo, contaminações por microrganismos. Estudos prévios indicaram que exsudatos dessas sementes apresentam substâncias com atividade antifúngica e fitotóxica e sugeriram também que oligossacarídeos oriundos da degradação do galactomanano agem como moléculas sinalizadoras de mecanismos de defesa em plantas. Entretanto, a liberação, natureza química e atividade biológica desses compostos ainda não haviam sido estudadas. Dessa forma, este trabalho teve por objetivos elucidar as estruturas químicas e estudar a exsudação de substâncias fitotóxicas e antifúngicas por sementes de S. virgata e H. courbaril, assim como, verificar a possível influência de oligossacarídeos derivados de galactomanano na produção desses metabólitos ativos em S. virgata. As sementes de S. virgata e H. courbaril foram germinadas em câmaras climatizadas à 25º C e fotoperíodo de 12 h e seus exsudatos foram coletados em diferentes períodos do processo de embebição, sendo posteriormente submetidos à bioensaios de fitotoxicidade com sementes de alface (Lactuca sativa L.) e de tomate (Solanum lycopersicum L.). Para o isolamento de compostos ativos, extratos dos exsudatos e extratos das sementes foram obtidos em larga escala através de extrações com solventes orgânicos, sendo, posteriormente, fracionados em colunas de gel de sílica utilizando gradientes de diclorometano e MeOH. As frações coletadas foram ensaiadas quanto a sua atividade fitotóxica em plântulas de Arabidopsis thaliana L. e de arroz (Oryza sativa L.) cultivadas in vitro. A atividade antifúngica dos extratos e frações foi determinada por métodos de bioautografia e microdiluição in vitro com fungos filamentosos e leveduras. As substâncias isoladas foram identificadas e caracterizadas por técnicas de 13C RMN e 1H RMN (1-D e 2-D). Quantificação e detecção de compostos também foram realizadas por análises em HPLC, HPLCMS e GC-MS. Os resultados obtidos demonstraram que ambas as sementes exsudam metabólitos secundários antifúngicos e fitotóxicos logo no início do processo de embebição. O flavonóide (+)-catequina é a principal fitotoxina dos exsudatos das sementes de S. virgata, sendo encontrada no tegumento das sementes e liberada em altas concentrações no primeiro dia de embebição. Quercetina também foi encontrada no tegumento das sementes de S. virgata, mas não é exsudada durante a germinação. Análises cromatográficas sugeriram a presença do alcalóide sesbanimida A nos extratos do embrião e nos exsudatos de S. virgata, como a principal substância antifúngica presente. Sementes de S. virgata embebidas em soluções contendo oligossacarídeos de galactomanano exsudaram maior quantidade de (+)-catequina do que aquelas embebidas apenas em água destilada, sugerindo que esses oligossacarídeos possam atuar como oligossacarinas sinalizadoras. Duas bicumarinas, a ipomopsina, anteriormente extraída de outra espécie vegetal e a himenaína, uma bicumarina inédita, foram isoladas de extratos do embrião das sementes de H. courbaril. Esses metabólitos também são exsudados durante a germinação e apresentam toxicidade às raízes de plântulas de A. thaliana quando co-aplicados e não apresentam atividade antifúngica, com exceção da escopoletina, também detectada nestes extratos. Entretanto, essas substâncias apresentaram atividade antioxidante, sendo himenaína a que apresentou maior capacidade seqüestradora do radical livre DPPH, sugerindo o envolvimento desses compostos na proteção a danos causados por radicais livres. Os dados obtidos neste trabalho sobre a atividade fitotóxica, antifúngica e antioxidante dos metabólitos isolados das sementes de S. virgata e H. courbaril sugerem que eles podem funcionar como estratégias adaptativas que contribuem para o sucesso do estabelecimento inicial dessas espécies. / Abstract: Sesbania virgata (Cav.) Pers. and Hymenaea courbaril L. var. stilbocarpa (Fabaceae) are two tropical legume species with seeds that contain galactomannan and xyloglucan, respectively, as seed storage polysaccharides, which are broken down after germination, generating large amounts of monosaccharides and oligosaccharides. Part of these sugars is released to the environment, but no contamination is observed. Previous studies demonstrated that these seed leachates have antifungal and phytotoxic activity and also suggested that oligosaccharides derived from galactomannan can act as signaling molecules in plant defense mechanisms. However, exudation, chemical structure and biological activities of the compounds have not been studied. Therefore, the aims of this work were to study the release of the bioactive compounds from seeds of S. virgata and H. courbaril, to elucidate their chemical structure and to analyze the influence of galactomannan oligosaccharides on the production of these substances in S. virgata. Seeds of S. virgata and H. courbaril were germinated at 25º C and photoperiod of 12 h, and the leachates were collected at different periods of the imbibition process, and submitted to phytotoxic bioassays with seeds of lettuce (Lactuca sativa L.) and tomato (Solanum ycopersicum L.). For compound isolation, extracts of seeds and leachates were obtained in large amounts and fractionated in silica gel columns with different gradient of dichloromethane and methanol. The fractions collected were assayed in vitro with seedlings of Arabidopsis thaliana L. and rice (Oryza sativa L.). The antifungal activity of the extracts and fractions were determined by bioautography and microdilution tests. The compounds were identified and characterized by 13C NMR and 1H NMR (1-D and 2-D) techniques. Compounds were also detected and quantified by HPLC, HPLC-MS and GC-MS. Our results showed that both seeds exude antifungal and phytotoxic metabolites at the beginning of imbibition process. The flavonoid (+)-catechin is the major phytotoxin in the S. virgata seed exudates, being found in the seed coat and leached in high amounts at the first day of imbibition. Quercetin was also found in the seed coat of S. virgata seeds, but it is not released during germination. The alkaloid sesbanimide A was detected in the embryo and exudates extracts of S. virgata, being the most important antifungal compound found in the extracts. Seeds of S. virgata imbibed with a galactomannan oligosaccharide solution leached more (+)-catechin than those imbibed in distilled water, suggesting that these molecules can act as oligosaccharins. Two biscoumarin, ipomopsin, previously reported in other plant species, and hymenain, a novel one, were identified in embryo extracts of H. courbaril. These compounds are also released by the seeds during germination, and showed a phytotoxic effect on roots of A. thaliana seedlings when co-applied, but they have not antifungal activity. Escopoletin were also detected in the embryo extracts, and showed antifungal activity to Cladosporium sphaerospermum Pemzig. Additionally, the biscoumarin and scopoletin, showed antioxidant activity, hymenain being the substance with higher scavenger activity to DPPH free radical, suggesting its involvement in the protection of the cells against free radical damages. Our findings related to the phytotoxic, antifungal, and antioxidant activities of metabolites isolated from seeds of S. virgata and H. courbaril suggest that they could act as adaptive strategies that contribute to the success of the initial establishment of these species. / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural

La contamination fongique des produits laitiers est à l’origine de pertes économiques conséquentes et de gaspillage alimentaire. Dans un contexte de demande pour plus de « naturalité », les cultures de bioprotection et leurs métabolites représentent une alternative d’intérêt aux conservateurs chimiques pour lutter contre ces contaminants.Les objectifs de cette thèse étaient i) de sélectionner des micro-organismes présentant une activité antifongique, pour élaborer des cultures de bioprotection applicables dans des produits laitiers, et ii) d’étudier les composés potentiellement supports de l’activité antifongique observée. Dans un premier temps, l’activité antifongique de 32 souches de bactéries lactiques et propioniques a été étudiée en modèles « fromage » et « yaourt ». L’étude de combinaisons de souches et de leur innocuité a conduit à sélectionner 2 combinaisons binaires de lactobacilles (A1 et A3). Leur efficacité et applicabilité a été évaluée à l’échelle pilote en fabrication de crème fraîche et de fromage.Les challenges tests et tests d’usages ont montré que selon le produit laitier, A1 et A3 ont une activité antifongique similaire ou supérieure que les cultures bioprotectrices commerciales. Selon l’inoculum ajouté, ces cultures n’impactent pas les caractéristiques technologiques et organoleptiques des produits laitiers. Des méthodes chromatographiques des composés antifongiques suivies d’analyses statistiques ont permis de mettre en évidence des « cocktails » de 2 à 17 composés, selon la matrice et la culture considérée, qui sont probablement supports de l’activité antifongique.Ces travaux contribuent à une meilleure compréhension des mécanismes d’action de l’activité antifongique et devraient conduire au développement de cultures antifongique pour remplacer les conservateurs dans les produits laitiers. / Fungal contamination of dairy products is responsible for economic losses and food waste. In a context of “preservative-free” product demand, bioprotective cultures and their metabolites represe,t an alternative of interest of chemical preservatives to control these spoilers.The objective of this study was i) to select microorganisms exhibiting an antifungal activity, in order to elaborate bioprotectivecultures applicable in dairy products, and ii) to study the compounds potentially supporting the observed activity. Firstly, the antifungal activity of 32 strains of lactic acid and propionic bacteria screened in cheese model and yogurt. Strain combinaison study and safety assessment led to the selection of 2 binary lactobacilli combinations (A1 and A3). Their efficiency and applicability were then evaluated in pilot-scale productions of sour cream and cheese.Challenge and shelf life tests showed that depending on the dairy product, A1 and A3 have a similar or higher antifungal activity than the commercial bioprotective cultures. In addition, depending of inoculum, A1 and A3 did not impact the technological and organoleptic characteristics. Chromatographic methods and statistical analyses allowed identifying cocktails of 2 to 17 compounds, according to the considered dairy product and culture that probably support the antifungal activity.The obtained results contribute to a better understanding of the antifungal activity action mechanisms and should lead to the development of antifungal cultures to replace preservatives in dairy products.

Orientador: Rinaldo Poncio Mendes / Resumo: A paracoccidioidomicose (PCM) é micose granulomatosa sistêmica causada por fungos termodimórficos do gênero Paracoccidioides. O presente estudo teve como objetivos avaliar a atividade da liriodenina, extraída de Annona macroprophyllata Donn. Sm, sobre isolados clínicos e cepas padrão de fungos do gênero Paracoccidioides e outras espécies que causam micoses sistêmicas e, através de um estudo-piloto realizado em modelo murino, avaliar a absorção da liriodenina e possíveis efeitos indesejáveis. A concentração inibitória mínima (CIM) e concentração fungicida mínima (CFM) da liriodenina foram determinadas pelo método de microdiluição. As alterações celulares causadas pela liriodenina em P. brasiliensis / cepa padrão Pb18 foram avaliadas pela microscopia eletrônica de transmissão (MET) e de varredura (MEV). Em estudo-piloto, quatro camundongos isogênicos albinos, da linhagem BALB/c, foram utilizados para avaliar a absorção e os efeitos indesejáveis da liriodenina. Os animais, sem infecção, foram divididos em dois grupos: grupo 1, com dois camundongos que receberam a dose de 0,75 mg.kg-1 e grupo 2, com dois camundongos que receberam a dose de 1,50 mg.kg-1, em única tomada. Após seis e 12 horas após a administração, os animais foram sacrificados e amostras de sangue foram coletadas para a determinação dos níveis séricos. Os intestinos foram coletados para exame histológico. O teste de sensibilidade in vitro revelou que a liriodenina possui atividade sobre parte dos fungos do gênero P... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Paracoccidioidomycosis (PCM) is systemic granulomatous mycosis caused by thermodymorphic fungi of the genus Paracoccidioides. The present study aimed to evaluate the activity of liriodenine, extracted from Annona macroprophyllata Donn. Sm on clinical isolates and standard strains of fungi of the genus Paracoccidioides and other species that cause systemic mycoses and, through a pilot study conducted in a murine model, to assess the absorption of liriodenine and possible undesirable effects. The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (CFM) of liriodenine were determined by the microdilution method. Cellular alterations caused by liriodenin in P. brasiliensis / Pb18 standard strain were evaluated by transmission electron microscopy (SEM) and scanning electron microscopy (SEM). In a pilot study, four albino isogenic mice of the BALB / c strain were used to assess the absorption and undesirable effects of liriodenine. The animals, without infection, were divided into two groups: group 1, with two mice receiving the dose of 0.75 mg.kg-1 and group 2, with two mice receiving the dose of 1.50 mg.kg- 1 , in single outlet. After six and 12 hours after administration, the animals were sacrificed and blood samples were collected for the determination of serum levels. The intestines were collected for histological examination. The in vitro sensitivity test revealed that liriodenine has activity on part of fungi of the genus Paracoccidioides, with MIC v... (Complete abstract click electronic access below) / Doutor

Submitted by Adriele Dandara Levorato Vinche (adrielelevorato@yahoo.com.br) on 2018-03-13T14:11:39Z No. of bitstreams: 1 Tese de Doutorado Adriele Dandara Levorato Vinche.pdf: 2200417 bytes, checksum: 23e69a47a9fa5126001d659e0803e67a (MD5) / Approved for entry into archive by Luciana Pizzani null (luciana@btu.unesp.br) on 2018-03-13T18:45:09Z (GMT) No. of bitstreams: 1 vinche_adl_dr_bot.pdf: 2200417 bytes, checksum: 23e69a47a9fa5126001d659e0803e67a (MD5) / Made available in DSpace on 2018-03-13T18:45:09Z (GMT). No. of bitstreams: 1 vinche_adl_dr_bot.pdf: 2200417 bytes, checksum: 23e69a47a9fa5126001d659e0803e67a (MD5) Previous issue date: 2018-02-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A paracoccidioidomicose (PCM) é micose granulomatosa sistêmica causada por fungos termodimórficos do gênero Paracoccidioides. O presente estudo teve como objetivos avaliar a atividade da liriodenina, extraída de Annona macroprophyllata Donn. Sm, sobre isolados clínicos e cepas padrão de fungos do gênero Paracoccidioides e outras espécies que causam micoses sistêmicas e, através de um estudo-piloto realizado em modelo murino, avaliar a absorção da liriodenina e possíveis efeitos indesejáveis. A concentração inibitória mínima (CIM) e concentração fungicida mínima (CFM) da liriodenina foram determinadas pelo método de microdiluição. As alterações celulares causadas pela liriodenina em P. brasiliensis / cepa padrão Pb18 foram avaliadas pela microscopia eletrônica de transmissão (MET) e de varredura (MEV). Em estudo-piloto, quatro camundongos isogênicos albinos, da linhagem BALB/c, foram utilizados para avaliar a absorção e os efeitos indesejáveis da liriodenina. Os animais, sem infecção, foram divididos em dois grupos: grupo 1, com dois camundongos que receberam a dose de 0,75 mg.kg-1 e grupo 2, com dois camundongos que receberam a dose de 1,50 mg.kg-1, em única tomada. Após seis e 12 horas após a administração, os animais foram sacrificados e amostras de sangue foram coletadas para a determinação dos níveis séricos. Os intestinos foram coletados para exame histológico. O teste de sensibilidade in vitro revelou que a liriodenina possui atividade sobre parte dos fungos do gênero Paracoccidioides, com valores de CIM entre 31,2 e 250 μg.mL-1 e sobre a cepa padrão de Histoplasma capsulatum (CIM de 1,95 μg.mL-1). No entanto, menor atividade foi observada em leveduras da maioria das espécies de Candida ensaiadas, com CIM de 125 a 250 μg.mL-1, e maior atividade sobre as cepas padrões de Cryptococcus neoformans e Cryptococcus gattii (CIM de 62,5 μg.mL-1), enquanto a cepa de Aspergillus fumigatus revelou-se resistente à maior concentração de liriodenina. Deve-se ressaltar a atividade da liriodenina sobre Candida krusei, que é intrinsecamente resistente ao fluconazol e, ao contrário, a ausência de atividade sobre Candida tropicalis. A liriodenina revelou ter atividade fungicida sobre todas as cepas padrão e isolados clínicos que foram inibidos in vitro. A MET revelou alterações citoplasmáticas e danos na parede celular de P.brasiliensis. O estudo-piloto revelou que, após 12 horas da administração da liriodenina, os animais que receberam a dose de 1,50 mg.kg-1 apresentavam gases intestinais e distensão abdominal, achados não observados nos que receberam 0,75 mg.kg-1. Os exames histológicos não evidenciaram alterações de intestino com nenhuma das doses empregadas. Níveis séricos de liriodenina foram detectados em ambos os grupos de animais. No entanto, os animais que receberam 0,75 mg.kg-1 de liriodenina apresentaram aumento da concentração com o passar do tempo, enquanto achado oposto foi observado nos que receberam 1,50 mg.kg-1. Os testes de sensibilidade in vitro indicaram que a liriodenina é uma alternativa promissora no tratamento de várias micoses sistêmicas. O estudo-piloto revelou que a liriodenina é absorvida após administração por gavagem, embora a dose de 1,50 mg.kg-1 tenha induzido alterações funcionais, caracterizadas por formação exagerada de gases e conseqüente distensão abdominal, que talvez possam explicar a diminuição de sua absorção. Os resultados do presente estudo estimulam a realização da avaliação da farmacocinética da liriodenina, de sua ação antifúngica em maior número de isolados de espécies de Candida spp, Cryptococcus spp, Histoplasma capsulatum e fungos do gênero Paracoccidioides e de sua eficácia em infecções experimentais em modelo murino. Por se tratar de composto antifúngico não pertencente às classes hoje utilizadas na terapia antifúngica, pode vir a contribuir com o tratamento de pacientes com infecções fúngicas resistentes. / Paracoccidioidomycosis (PCM) is systemic granulomatous mycosis caused by thermodymorphic fungi of the genus Paracoccidioides. The present study aimed to evaluate the activity of liriodenine, extracted from Annona macroprophyllata Donn. Sm on clinical isolates and standard strains of fungi of the genus Paracoccidioides and other species that cause systemic mycoses and, through a pilot study conducted in a murine model, to assess the absorption of liriodenine and possible undesirable effects. The minimum inhibitory concentration (MIC) and minimum fungicidal concentration (CFM) of liriodenine were determined by the microdilution method. Cellular alterations caused by liriodenin in P. brasiliensis / Pb18 standard strain were evaluated by transmission electron microscopy (SEM) and scanning electron microscopy (SEM). In a pilot study, four albino isogenic mice of the BALB / c strain were used to assess the absorption and undesirable effects of liriodenine. The animals, without infection, were divided into two groups: group 1, with two mice receiving the dose of 0.75 mg.kg-1 and group 2, with two mice receiving the dose of 1.50 mg.kg- 1 , in single outlet. After six and 12 hours after administration, the animals were sacrificed and blood samples were collected for the determination of serum levels. The intestines were collected for histological examination. The in vitro sensitivity test revealed that liriodenine has activity on part of fungi of the genus Paracoccidioides, with MIC values between 31.2 and 250 μg.mL-1 and on the standard Histoplasma capsulatum strain (MIC of 1.95 μg .mL-1 ). However, lower activity was observed in yeasts of most Candida species tested, with MIC of 125 to 250 μg.mL-1 , and greater activity on the standard strains of Cryptococcus neoformans and Cryptococcus gattii (MIC of 62.5 μg. mL-1 ), while the strain of Aspergillus fumigatus was resistant to the highest concentration of liriodenine. The activity of liriodenine on Candida krusei, which is intrinsically resistant to fluconazole and, on the contrary, the absence of activity on Candida tropicalis should be emphasized. Liriodenin reveale over all standard strains and clinical isolates that were inhibited in vitro. MET showed cytoplasmic alterations and damage to P. brasiliensis cell wall. The pilot study revealed that animals receiving the 1.50 mg.kg-1 dose had no intestinal gas and abdominal distension 12 hours after administration of liriodenine, which were not observed in those receiving 0.75 mg.kg-1 . Histological examinations showed no intestinal changes at any of the doses used. Serum levels of liriodenine were detected in both groups of animals. However, animals receiving 0.75 mg.kg-1 liriodenine showed increased concentration over time, while the opposite finding was observed in those receiving 1.50 mg.kg-1 . In vitro sensitivity tests indicated that liriodenine is a promising alternative in the treatment of various systemic mycoses. The pilot study revealed that liriodenine is absorbed after administration by gavage, although the 1.50 mg.kg-1 dose induced functional alterations, characterized by exaggerated gas formation and consequent abdominal distension, which may explain the decrease of its absorption. The results of the present study stimulate the evaluation of the pharmacokinetics of liriodenine, its antifungal action in a greater number of isolates of Candida species, Cryptococcus spp, Histoplasma capsulatum and fungi of the genus Paracoccidioides and their efficacy in experimental infections in murine model. Because it is an antifungal compound that does not belong to the classes currently used in antifungal therapy, it may contribute to the treatment of patients with resistant fungal infections.

The aim of this study was to isolate and characterize antifungal compounds from the most active medicinal plant species that could be used to address secondary infection problems in immunocompromised patients. An ethnobotanical study was conducted and 45 medicinal plant species used traditionally to treat candidiasis and related infections in HIV/AIDS patients were identified and documented. The most popular plant species used included Acacia caffra, Clerodendrum glabrum, Croton gratissimus, Elaeodendron transvaalense, Faurea saligna, Hippocratea longipetiolata, Osyris lanceolata, Richardia brasiliensis, Schkuhria pinnata, Schotia brachypetala, Spilanthes acmella, Strychnos potatorum, Vangueria infausta subsp. infausta and Withania somnifera. The plant parts used in the therapeutic preparations were roots (26.7%), bark (22.2%), and a combination of roots and bark (17.7%). Decoctions (44.4%), infusions (20%) and macerations (17.7%) were used. Most of the herbal remedies were administered orally. Chemical profiles of the plant species were established by using thin layer chromatography. Leaf extracts of these plant species were tested for antimicrobial activity against two common pathogenic fungal species in humans (Candida albicans and Cryptococcus neoformans) and four nosocomial bacteria (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli and Pseudomonas aeruginosa) using a two-fold serial microdilution method and bioautography. All plant species investigated had some degree of antimicrobial activity against the test microorganisms. The hexane and the acetone extracts of Clerodendrum glabrum, Hippocratea longipetiolata, Schkuhria pinnata and Withania somnifera were the most active with MIC values ranging from 0.06 to 0.08 mg/ml. The most susceptible pathogen to the test samples was C. neoformans while C. albicans was resistant to most of the plant extracts. The water extracts of Withania somnifera and Hippocratea longipetiolata (14%) had MIC < 1 mg/ml against C. albicans. C. neoformans was susceptible to nine water plant extracts (64%) with MIC < 1 mg/ml and the promising activity was observed in Hippocratea longipetiolata and Faurea saligna extracts with MIC values of 0.16 and 0.31 mg/ml respectively. The hexane extract of C. glabrum was the most active against C. albicans with an MIC value of 0.06 mg/ml and total activity of 550 ml/g. In the bioautography, most plant extracts tested had few active compounds, others had no active components at all and this may be attributed to the disruption of synergism by the thin layer chromatography. C. glabrum had eight active antifungal compounds on bioautograms and most of these components were observed in the EMW solvent system. Based on this and its wide distribution in rural areas, C. glabrum was chosen for further study. The antioxidant activity and possible immune boosting potential of the species were determined using 1, 1-diphenyl-2-picrylhydrazyl radical (DPPH), 2, 2’ azinobis-(3-ethylbenzthiazoline-6-sulfonic acid (ABTS) and ferric reducing antioxidant power (FRAP) assays. In the DPPH qualitative assay, the aqueous plant extracts had several prominent antioxidant components than the organic plant extracts. The aqueous plant extracts which had the most prominent antioxidant activity were F. saligna with 8 compounds, followed by E. transvaalense, H. longipetiolata O. lanceolata, R. brasiliensis and S.brachypetala, with five compounds each and their Rf values ranged from 0;06 to 0.94. This appears to validate the ethnomedicinal use of the plant species to some extent because decoction is the most common method used in the preparation of the remedy by the traditional healers. With regard to the organic plant extracts, only one plant extract, F. saligna had two prominent antioxidant components at Rf values 0.81 and 0.88. A third of the plant species had a high level of free radical scavenging activities in the DPPH, ABTS and FRAP assays. However, all plant extracts had lower antioxidant activity than the positive control (Trolox) used. The selected plant species were also evaluated for their in vitro toxicity against the Vero monkey kidney cell line using 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide (MTT) assay. The acetone plant extracts of O. lanceolata, S. acmella, S. pinnata and S. brachypetala had high cytotoxic activity against Vero cells with IC50 values of 13.7±0, 19.9±0.001, 21.6±0.001 and 28.34±0.001 μg/ml respectively. However, their IC50 values were higher than that of the positive control, doxorubicin (IC50 = 9.9±0 μg/ml). The rest of the acetone plant extracts (64%) had moderate cytotoxic activity (30 < IC50<100 μg/ml). The aqueous plant extracts were relatively non-toxic to the Vero cells with IC50 values ranging from 137 to > 500 µg/ml. This supports the use of aqueous extracts in the traditional medicine. However, their low selectivity index values ranging from 0.26 to 1.68 suggest that the plant extracts are probably suitable for external use only. Fractionation of the hexane extract of the leaves of C. glabrum by chromatographic techniques yielded six fractions of which fractions C and D had significant antifungal activity (average MIC value = 0.1 mg/ml) against C. albicans and C. neoformans. From these fractions, one new triterpenoid, 3-(1-oxobutyl)-11α-hydroxytaraxast-20(30)-ene-24,28-dioic acid (clerodendrumic acid) (1) was isolated along with known heptadecanoic acid (2). C. albicans was relatively insensitive to clerodendrumic acid (1) (MIC value = 125 µg/mL) and was resistant to heptadecanoic acid (2) (MIC value = 188 µg/ml). Compounds 1 and 2 were non-toxic against monkey kidney Vero cells in vitro with IC50 values of 202.6 and 108.4 µg/ml respectively. Due to its low antifungal activity, the novel compound clerodendrumic acid (1) is not a viable candidate for drug development which could be used to combat candidiasis and related fungal infections. However, due to its relative safety, it may possibly be used as a lead compound to produce new chemically modified active derivatives or could be used together with known antibiotics to mitigate their undesirable side effects. To the best of our knowledge, the isolation of a novel, clerodendrumic acid (1) and a known heptadecanoic acid (2) compounds from leaf extracts of C. glabrum is reported herein for the first time. The results obtained from this study generally substantiate the rationale behind the use of the selected plant species in the traditional medicine to treat candidiasis and related infections to some extent. This study showed the potential of studying traditional medicine in the search for effective plant extracts or new lead compounds that could be developed into drugs for combating microbial infections among the rural poor people. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Paraclinical Sciences / Unrestricted