Orientador: Katia Sivieri / Orientador no exterior: Lene Jespersen / Banca: Suzana Marta Isay Saad / Banca: Adriane Elisabete Antunes de Moraes / Banca: Carla Raquel Fontana Mendonça / Banca: Marcia Pinto Alves Mayer / Resumo: Diversos subprodutos de frutas tropicais, os quais são frequentemente descartados pelas indústrias alimentícias, apresentam elevado conteúdo de fibras e de compostos bioativos. Estes compostos, assim como determinadas cepas probióticas e algumas pectinas presentes nos subprodutos, têm o potencial de modular a microbiota intestinal humana, promovendo diversos benefícios à saúde, tais como a atenuação de parâmetros relacionados à obesidade. O objetivo deste trabalho foi avaliar os efeitos da pectina do limão, de subprodutos secos de frutas tropicais (acerola e camu-camu) e de diferentes cepas probióticas (Bifidobacterium longum BB-46, Lactobacillus acidophilus LA-5 and L. paracasei L-431) na microbiota intestinal de indivíduos eutróficos e obesos utilizando o Simulador do Ecossistema Microbiano Humano (SEMH®). Seis artigos foram desenvolvidos a fim de se responder os objetivos propostos. O primeiro artigo trata-se de uma mini-revisão e, os cinco restantes, artigos originais. No primeiro artigo, sumarizou-se os principais achados sobre a composição da microbiota intestinal de obesos e, revisou-se as novas estratégias de modulação da microbiota intestinal em favor do tratamento da obesidade. Foi possível mostrar que a composição da microbiota intestinal é essencial para o entendimento de mecanismos envolvidos na etiologia da obesidade e que, várias estratégias, tais como, o consumo de prebióticos e probióticos, bem como a prática de atividade física moderada e regular, podem modu... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Several by-products of tropical fruits, which are often discarded by the food industry, have high fibre content and bioactive compounds. These compounds, as well as certain probiotic strains and some pectins present in the by-products, have the potential to modulate the human gut microbiota, promoting several health benefits, including the attenuation of obesity parameters. The aim of this work was to evaluate the effects of lemon pectin, dried by-products of tropical fruits (acerola and camu-camu), as well as of different probiotic strains (Bifidobacterium longum BB-46, Lactobacillus acidophilus LA-5 and L. paracasei L-431) on the gut microbiota from healthy-weight and obese individuals using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Six articles were developed in order to meet the proposed aims. The first article is a mini-review and the other five are original articles. In the first article, we summarized the principal findings on obesity-related microbiota composition and reviewed new strategies for gut microbiota modulation in favour of obesity treatment. We showed that the composition of the microbiota is essential for understanding the mechanisms involved in the aetiology of obesity and, that several strategies, such as consumption of probiotics and prebiotics, as well as moderate and regular physical activity, can modulate the gut microbiota in favour of obesity treatment. In the second article, the chemical composition, the total phenolic co... (Complete abstract click electronic access below) / Resumé: Flere biprodukter fra tropiske frugter, som ofte kasseres af fødevareindustrien, har højt fiberindhold og bioaktive forbindelser. Disse forbindelser, såvel som visse probiotiske stammer og nogle pektiner, der er til stede i biprodukterne, har potentialet til at modulere den humane tarmmikrobiota, der fremmer flere sundhedsmæssige fordele, herunder dæmpning af fedmeparametre. Formålet med dette arbejde var at evaluere virkningerne af citronpektin, tørrede biprodukter fra tropiske frugter (acerola og camu-camu), samt forskellige probiotiske stammer (Bifidobacterium longum BB-46, Lactobacillus acidophilus LA-5 og L. paracasei L-431) på tarmmikrobioten fra raske og overvægtige individer, under anvendelsen af den humane intestinale mikrobielle økosystem simulator (SHIME®). Seks artikler blev udviklet for at opfylde de foreslåede mål. Den første artikel er en mini-anmeldelse, og de andre fem er originale artikler. I den første artikel opsummerede vi de vigtigste fund om fedme-relateret mikrobiota sammensætning og gennemgik nye strategier for tarmmikrobiota modulering til fordel for fedmebehandling. Vi viste, at mikrobiotas sammensætning er afgørende for forståelsen af mekanismerne i fedmens etiologi, og at flere strategier, såsom forbrug af probiotika og præbiotika, samt moderat og regelmæssig fysisk aktivitet kan modulere tarmmikrobiotaten til fordel for fedme behandling. I det anden artikel blev den kemiske sammensætning, de samlede phenolforbindelser og in vitro antioxidantkapac / Doutor

Introduction: Diabetes is a global and rapidly increasing disease that in 2014 affected morethan 422 million people, and takes 1,2 million lives per year. The importance of identifyingnew ways to manage and prevent the disease has led science to a new area – modulation ofthe gut microbiota. It is well known that the composition of gut microbiota differs betweennon-diabetic and diabetic adults, and that nutrition is the main way to modulate gutmicrobiota composition. Food and lifestyle are of great importance for the development andtreatment of type 2 diabetes and pre-diabetes, but less is known about whether gut microbiotamodulation is mediating that link. Aim: The aim is to examine whether there is a scientifically well-supported link between diet,gut microbiota and the development or treatment of type 2 diabetes or pre-diabetes in humans. Methods: Systematic review with literature search via PubMed and Cochrane, following themanual from the Swedish Agency for Health Technology Assessment and Assessment ofSocial Services (SBU). Results: Of 12 articles finally included, two studies found a strong impact of diet on diabetesrelatedvariables via modulation of gut microbiota. Another four studies did not find anassociation, and six studies lacked sufficient data to be able to draw a conclusion. Dietinterventions and study design differed between studies, which led to heterogeneous results. Conclusions: This review demonstrates a large knowledge gap in how dietary modificationscan prevent or treat type 2 diabetes or pre-diabetes via changes in gut microbiota.

The application of second generation sequencing technology to the characterization of complex microbial communities has profoundly affected our appreciation of microbial diversity. The explosive growth of microbial sequence data has also necessitated advances in bioinformatic methods for profiling microbial communities. Data aggregation strategies should allow the relation of metagenomic sequence data to our understanding of microbial taxonomy, while also facilitating the discovery of novel taxa. For eukaryotes, a method has been established that links DNA sequences to the identification of organisms: DNA Barcoding. A similar approach has been developed for prokaryotes using target genic regions as markers for species identification and to profile communities. A key difference in these efforts is that within DNA barcoding there is a formalized framework for the evaluation of barcoding targets, whereas for prokaryotes the 16S rRNA gene target has become the de facto barcode without formal evaluation. Using the framework developed for evaluating DNA barcodes in eukaryotes, a study was undertaken to formally evaluate 16S rRNA and cpn60 as DNA barcodes for Bacteria. Both 16S rRNA and cpn60 were found to meet the criteria for DNA barcodes, with cpn60 a preferred barcode based on its superior resolution of closely related taxa. The high resolution of cpn60 enabled a method of sequence data aggregation through sequence assembly: microbial profiling using metagenomic assembly (mPUMA). The scoring of metagenomic assemblies in terms of sensitivity and specificity of the operational taxonomic units formed was used to evaluate and optimize the assembly of cpn60 barcodes. Using optimized parameters, mPUMA was demonstrated to faithfully reconstruct a synthetic community in terms of richness and abundance. To facilitate the use of mPUMA, a software package was developed and released under an open source license. The utility of mPUMA was further examined through the characterization of the epiphytic seed microbiomes of Triticum and Brassica species. A microbiome shared across both crop genera including fungi and bacteria was detected: a particularly important observation as it implies that seeds may serve as a vector for microbes that could include both pathogenic and beneficial organisms. The relative abundances of taxa identified by mPUMA were confirmed by qPCR for multiple cases of both fungal and bacterial taxa. By culturing isolates of both bacteria and fungi from the seed surfaces it was demonstrated that mPUMA faithfully assembled consensus sequences for OTUs that were 100% identical to isolated fungi and bacteria. Patterns observed in the relative abundances of the shared microbiome OTUs were used to generate the hypothesis that an Pantoea-like bacterium and an Alternaria-like fungus had an antagonistic relationship, since sequences corresponding to these organisms showed reciprocal abundance patterns on Triticum and Brassica seeds. Studies of the interactions of cultured isolates revealed fungistatic interactions that could account for their reciprocal abundances. These interactions could be directly relevant to plant health, given that Alternaria-like fungi are linked to grain spoilage in wheat, and diseases in canola. Taken together, results of this thesis demonstrate the superiority of the cpn60 universal target as a barcode for Bacteria, forming the basis for an assembly-based strategy for microbial profiling of bacterial and eukaryotic microbial communities that can lead to the discovery of novel taxa and microbial interactions.

<p>Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli and significant players in the ecology and physiology of lichens. Despite recent interest in this topic, the phylogeny, ecology, and function of these bacteria remain largely unknown. The experiments presented in this dissertation employ culture-free methods to examine the bacteria housed in these unique environments to ultimately inform an assessment of their status with regard to the lichen symbiosis. Microbiotic surveys of lichen thalli using new oligonucleotide-primers targeting the 16S SSU rRNA gene (developed as part of this study to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria) revealed the identity of diverse bacterial associates, including members of an undescribed lineage in the order Rhizobiales (Lichen-Associated Rhizobiales 1; `LAR1'). It is shown that the LAR1 bacterial lineage, uniquely associated with lichen thalli, is widespread among lichens formed by distantly related lichen-forming fungi and is found in lichens collected from the tropics to the arctic. Through extensive molecular cloning of the 16S rRNA gene and 454 16S amplicon sequencing, ecological trends were inferred based on mycobiont, photobiont, and geography. The implications for using lichens as microcosms to study larger principles of ecology and evolution are discussed. In addition to phylogenetic and ecological studies of lichen-associated bacterial communities, this dissertation provides a first assessment of the functions performed by these bacteria within the lichen microbiome in nature through 454 sequencing of two different lichen metatranscriptomes (one from a chlorolichen, <italic>Cladonia grayi</italic>, and one from a cyanolichen, <italic>Peltigera praetextata</italic>). Non-photobiont bacterial genes for nitrogen fixation were not detected in the <italic>Cladonia</italic> thallus (even though transcripts of cyanobacterial nitrogen fixation genes from two different pathways were detected in the cyanolichen thallus), implying that the role of nitrogen fixation in the maintenance of chlorolichens might have previously been overstated. Additionally, bacterial polyol dehydrogenases were found to be expressed in chlorolichen thalli (along with fungal polyol dehydrogenases and kinases from the mycobiont), suggesting the potential for bacteria to begin the process of breaking down the fixed carbon compounds secreted by the photobiont for easier metabolism by the mycobiont. This first look at the group of functional genes expressed at the level of transcription provides initial insights into the symbiotic network of interacting genes within the lichen microbiome.</p> / Dissertation

Abstract Based on maintaining healthy soil for sustainable agriculture and enhancing banana disease resistance, Taiwan Banana Research Institute began to conduct organic cultivation on a trial basis in 1998. It had been proved that the morbidity of banana Fusarial wilt disease at organic cultivation plots was significantly lower than that of conventional farming. In order to study the differences of soil microbiota between the organic cultivation plots and the conventional farming areas, physical and chemical properties of the rhizosphere and non- rhizosphere soil samples were assayed during the period of Aug. 2010 to May 2011. The bacterial diversity was analyzed by molecular biology methods, including PCR-DGGE to separate the 16S rDNA V6 ~ V8 region of various bacteria and the recombinant DNA technology by using pGEM-T Easy Vector System to separate and sequence the DNA fragments. The results showed that organic plots was loam soil, but the conventional farming soil was sandy loam with higher sand content. The soil pH in 13 years organic area was mildly alkaline, but in conventional farming area was mildly acidic to slightly acidic. The content of various nutrients in organic 13-year area soil was not necessarily higher than the conventional farming area soil. The available nutrient contents in organic areas trend to be more stable than that in the conventional areas. Fertilization may affect the content of available nutrients in the soil. No bacterial DNA could be extracted from the organic fertilizer. The bacterial microbiota in soil was very stable, and was not related to the sampling seasons. The Banana strains had little effect on soil bacterial microbiota. There was no difference on the bacterial microbiota between the rhizosphere and non-rhizosphere soil samples. It is not sure whether there were any differences on the bacterial microbiota between the nearby soil of banana Fusarial wilt plants and the nearby soil of the healthy plants. By analyzing the DNA fragment clone library, 43 strains correspond to known category, of which 28 belonged to the Proteobacteria, and 34 were uncultured strains. The role of these microbial strains might involve in various element cycles, such as N cycles, C cycles, and S cycles (including some photosynthetic bacteria). The systematic cladogram showed that organic 13-year areas, organic 3-year areas and conventional farming areas represented three major categaries. The organic 13-year area and conventional area possessed the highest difference on the microbiota composition.

Hintergrund: Gestillte Kinder haben im Vergleich zu nicht gestillten Kindern eine geringere Inzidenz von gastrointestinalen Infektionen und atopischen Erkrankungen. Man geht davon aus, dass der gesundheitsfördernde Effekt der Muttermilch teilweise über die intestinale Mikrobiota vermittelt wird. Diese ist in Stillkindern durch eine geringe Diversität und einen hohen Anteil an Bifidobakterien charakterisiert. Neueste Ansätze in der Weiterentwicklung industriell hergestellter Säuglingsnahrung zielen darauf ab, eine intestinale Mikrobiota zu fördern, die der von gestillten Kindern ähnelt. Die Supplementation von Säuglingsnahrung mit Probiotika (lebende Mikroorganismen) oder Präbiotika (unverdauliche Kohlenhydrate, die als Energiesubstrat für probiotische Bakterien dienen) könnte die bifidogene und antipathogene, aber auch immunmodulierende Wirkung der Muttermilch nachahmen. Aufgrund unterschiedlicher Interaktionen mit der Darmmikrobiota und dem Immunsystem fokussiert man mit der gleichzeitigen Gabe von Pro- und Präbiotika (Synbiotika) eine synergistische Wirkung an. Zielstellung und Studiendesign: In einer randomisiert-kontrollierten, klinischen Studie wurde untersucht, ob sich in den ersten drei Lebensmonaten von gesunden und termingerecht geborenen Kindern mit einer Synbiotikum-haltigen Säuglingsnahrung eine intestinale Mikrobiota etabliert, die der von gestillten Kindern gleicht. Das Synbiotikum setzte sich aus Bifidobacterium animalis ssp. lactis CNCM I 3446 (ältere Bezeichnung B. lactis BB-12) und Kuhmilcholigosacchariden zusammen. Die Studie umfasste zwei Gruppen von Kindern, die eine Säuglingsnahrung mit (SYN-Gruppe, n=21) oder ohne Supplement (KON-Gruppe, n=18) erhielten. Gestillte Kinder dienten als Referenz (REF-Gruppe, n=23). Um die Diversität der Bifidobakterien auf Speziesebene umfassend zu charakterisieren, wurden quantitative Real-Time PCR (qPCR)-Verfahren, basierend auf dem single-copy groEL als phylogenetisches Zielgen, zur spezifischen Quantifizierung von zwölf Bifidobakterienspezies in humanen Fäzes entwickelt und validiert. Ergebnisse: Die supplementierte Säuglingsnahrung war gut verträglich und unterstützte eine gesunde Entwicklung; vergleichbare anthropometrische Daten von SYN- und REF-Gruppe. Das Synbiotikum stimulierte selektiv das Wachstum von Laktobazillen und Bifidobakterien. Die Zellzahl für Laktobazillen der SYN-Gruppe war zur REF-Gruppe äquivalent (9,07±0,32 versus 9,90±0,27 log10 Zellen/g Fäzes TM [MW±SEM]; p<0,0019; Äquivalenzdifferenz von 1 log10 Zellen/g Fäzes TM) und höher als in der KON-Gruppe (8,27±0,31 log10 Zellen/g Fäzes TM [MW±SEM]). Die Zellzahl für Bifidobakterien war in der SYN-Gruppe am höchsten (11,54±0,05 versus 11,00±0,17 [REF-Gruppe] und 10,54±0,24 [KON-Gruppe] log10 Zellen/g Fäzes TM [MW±SEM]). In der SYN-Gruppe wurde die höchste Anzahl an Bifidobakterienspezies erfasst (167 mit [128 ohne] B. animalis in 56 Fäzesproben versus 98 und 93 in jeweils 51 Fäzesproben der REF- und KON-Gruppe). Neben Kinder-typischen Spezies wie B. bifidum und B. breve wurden auch Spezies, die für Erwachsene charakteristisch sind (B. adolescentis), häufiger in der SYN-Gruppe als in den Vergleichsgruppen nachgewiesen. Der pH-Wert in Fäzes von Kindern aus der SYN-Gruppe war niedriger als der aus der KON-Gruppe (6,07±0,20 versus 6,45±0,17 [MW±SEM]) und näher an dem von gestillten Kindern mit 5,29±0,12 (MW±SEM). Schlussfolgerung: Die Supplementation einer Säuglingsnahrung mit dem Synbiotikum aus CNCM I-3446 und Kuhmilcholigosacchariden führte zu einer Angleichung in der Zusammensetzung der intestinalen Mikrobiota und des fäkalen pH-Wertes an gestillte Kinder. Die in dieser Arbeit entwickelten groEL-basierten qPCR-Verfahren erlaubten eine spezifische und genaue Analyse der Bifidobakterienpopulation unter dem Einfluss eines Synbiotikums. / Background: Compared to formula-fed infants, breast-fed infants have a reduced incidence of gastrointestinal infections and atopic diseases. The health-promoting effect of breast milk is assumed to be partly mediated by the intestinal microbiota, which is characterized by a low diversity and a high proportion of bifidobacteria. Recent approaches in further development of infant formulae aim at promoting an intestinal microbiota similar to that of breast-fed infants. The supplementation of infant formula with probiotics (live microorganisms) or prebiotics (non-digestible carbohydrates, which serves as energy substrates for probiotic bacteria) could mimic the bifidogenic and antipathogenic, but also immunomodulating effect of breast milk. Due to various interactions with the gut microbiota and the immune system, the simultaneous administration of pro- and prebiotics (synbiotics) is focussed to have a synergistic effect. Objective and study design: In a randomized-controlled, clinical trial healthy full-term infants receiving an infant formula with synbiotic for the first three months of life were studied, whether an intestinal microbiota is induced, which is equivalent to that of breast-fed infants. The synbiotic consisted of Bifidobacterium animalis ssp. lactis CNCM I 3446 (previously known as B. lactis BB-12) and cow milk oligosaccharides. The study comprised two groups of infants receiving a starter formula with (SYN-group, n=21) or without supplement (KON-group, n=18). Breast-fed infants served as a reference (REF-group, n=23). In order to comprehensively characterize the bifidobacteria diversity at species level, quantitative real-time PCR (qPCR) assays based on the single-copy groEL as phylogenetic marker for the specific quantification of twelve bifidobacteria species in human feces were established and validated. Results: The supplemented formula was well tolerated and supported a healthy development; comparable anthropometric data of SYN- and REF-group. The synbiotic selectively stimulated the growth of lactobacilli and bifidobacteria. Lactobacilli levels were equivalent in SYN- and REF-group (9.07±0.32 versus 9.90±0.27 log10 cells/g feces DM [Mean±SEM]; p<0.0019; equivalence margin of 1 log10 cells/g feces DM) and higher than the KON-group (8.27±0.31 log10 cells/g feces DM [Mean±SEM]). The highest levels of bifidobacteria were observed in the SYN-group (11.54±0.05 versus 11.00±0.17 [REF-group] and 10.54±0.24 [KON-group] log10 cells/g feces DM [Mean±SEM]). The highest number of bifidobacteria species were obtained in the SYN-group (167 with [128 without] B. animalis in 56 fecal samples versus 98 and 93 in each of 51 fecal samples of the REF- and KON-group). Beside species, typically found in infants such as B. bifidum und B. breve, also species, which are characteristic for adults (B. adolescentis), were detected more often in the SYN-group than in the other study groups. Fecal pH was lower in the SYN- than in the KON-group 6.07±0.20 versus 6.45±0.17 [Mean±SEM]) and closer to that of breast-fed infants (5.29±0.12 [Mean±SEM]). Conclusion: In infants fed a starter formula supplemented with a synbiotic (CNCM I-3446 and cow milk oligosaccharides), composition of intestinal microbiota and fecal pH were closer to that of breast-fed infants. The groEL-based qPCR-assays, developed in this study, allowed a specific and accurate analysis of the bifidobacterial population in response to the synbiotic intake.

Diet is a major force influencing the intestinal microbiota. This is obvious from drastic changes in microbiota composition after a dietary alteration. Due to the complexity of the commensal microbiota and the high inter-individual variability, little is known about the bacterial response at the cellular level. The objective of this work was to identify mechanisms that enable gut bacteria to adapt to dietary factors. For this purpose, germ-free mice monoassociated with the commensal Escherichia coli K-12 strain MG1655 were fed three different diets over three weeks: a diet rich in starch, a diet rich in non-digestible lactose and a diet rich in casein. Two dimensional gel electrophoresis and electrospray tandem mass spectrometry were applied to identify differentially expressed proteins of E. coli recovered from small intestine and caecum of mice fed the lactose or casein diets in comparison with those of mice fed the starch diet. Selected differentially expressed bacterial proteins were characterised in vitro for their possible roles in bacterial adaptation to the various diets. Proteins belonging to the oxidative stress regulon oxyR such as alkyl hydroperoxide reductase subunit F (AhpF), DNA protection during starvation protein (Dps) and ferric uptake regulatory protein (Fur), which are required for E. coli’s oxidative stress response, were upregulated in E. coli of mice fed the lactose-rich diet. Reporter gene analysis revealed that not only oxidative stress but also carbohydrate-induced osmotic stress led to the OxyR-dependent expression of ahpCF and dps. Moreover, the growth of E. coli mutants lacking the ahpCF or oxyR genes was impaired in the presence of non-digestible sucrose. This indicates that some OxyR-dependent proteins are crucial for the adaptation of E. coli to osmotic stress conditions. In addition, the function of two so far poorly characterised E. coli proteins was analysed: 2 deoxy-D gluconate 3 dehydrogenase (KduD) was upregulated in intestinal E. coli of mice fed the lactose-rich diet and this enzyme and 5 keto 4 deoxyuronate isomerase (KduI) were downregulated on the casein-rich diet. Reporter gene analysis identified galacturonate and glucuronate as inducers of the kduD and kduI gene expression. Moreover, KduI was shown to facilitate the breakdown of these hexuronates, which are normally degraded by uronate isomerase (UxaC), altronate oxidoreductase (UxaB), altronate dehydratase (UxaA), mannonate oxidoreductase (UxuB) and mannonate dehydratase (UxuA), whose expression was repressed by osmotic stress. The growth of kduID-deficient E. coli on galacturonate or glucuronate was impaired in the presence of osmotic stress, suggesting KduI and KduD to compensate for the function of the regular hexuronate degrading enzymes under such conditions. This indicates a novel function of KduI and KduD in E. coli’s hexuronate metabolism. Promotion of the intracellular formation of hexuronates by lactose connects these in vitro observations with the induction of KduD on the lactose-rich diet. Taken together, this study demonstrates the crucial influence of osmotic stress on the gene expression of E. coli enzymes involved in stress response and metabolic processes. Therefore, the adaptation to diet-induced osmotic stress is a possible key factor for bacterial colonisation of the intestinal environment. / Sowohl Humanstudien als auch Untersuchungen an Tiermodellen haben gezeigt, dass die Ernährung einen entscheidenden Einfluss auf die Zusammensetzung der Darmmikrobiota hat. Aufgrund der Komplexität der Mikrobiota und der inter individuellen Unterschiede sind die zellulären Mechanismen, die dieser Beobachtung zugrunde liegen, jedoch weitgehend unbekannt. Das Ziel dieser Arbeit war deshalb, Anpassungsmechanismen von kommensalen Darmbakterien auf unterschiedliche Ernährungsfaktoren mittels eines simplifizierten Modells zu untersuchen. Dazu wurden keimfreie Mäuse mit Escherichia coli MG1655 besiedelt und drei Wochen mit einer stärkehaltigen, einer laktosehaltigen oder einer kaseinhaltigen Diät gefüttert. Mittels zwei dimensionaler Gelelektrophorese und Elektrospray Ionenfallen-Massenspektrometrie wurde das Proteom der intestinalen E. coli analysiert und differentiell exprimierte bakterielle Proteine in Abhängigkeit der gefütterten Diät identifiziert. Die Funktion einiger ausgewählter Proteine bei der Anpassung von E. coli auf die jeweilige Diät wurde im Folgenden in vitro untersucht. E. coli Proteine wie z.B. die Alkylhydroperoxid Reduktase Untereinheit F (AhpF), das DNA Bindeprotein Dps und der eisenabhängige Regulator Fur, deren Expression unter der Kontrolle des Transkriptionsregulators OxyR steht, wurden stärker exprimiert, wenn die Mäuse mit der laktosehaltigen Diät gefüttert wurden. Reportergenanalysen zeigten, dass nicht nur oxidativer Stress, sondern auch durch Kohlenhydrate ausgelöster osmotischer Stress zu einer OxyR abhängigen Expression der Gene ahpCF and dps führte. Weiterhin wiesen E. coli Mutanten mit einer Deletion der ahpCF oder oxyR Gene ein vermindertes Wachstum in Gegenwart von nicht fermentierbarer Saccharose auf. Das spricht dafür, dass OxyR abhängige Proteine eine wichtige Rolle bei der Anpassung von E. coli an osmotischen Stress spielen. Weiterhin wurde die Funktion von zwei bisher wenig charakterisierten E. coli Proteinen untersucht: die 2 Deoxy D Glukonate 3 Dehydrogenase (KduD) wurde im Darm von Mäusen, die mit der laktosehaltigen Diät gefüttert wurden, induziert, während dieses Protein und die 5 Keto 4 Deoxyuronate Isomerase (KduI) nach Fütterung der kaseinhaltigen Diät herunterreguliert wurden. Mittels Reportergenanalysen wurde gezeigt, dass Galakturonat und Glukuronat die kduD und kduI Expression induzierten. KduI begünstigte die Umsetzung dieser Hexuronate. In E. coli wird die Umsetzung von Galakturonat und Glukuronat typischerweise von den Enzymen Uronate Isomerase (UxaC), Altronate Oxidoreduktase (UxaB), Altronate Dehydratase (UxaA), Mannonate Oxidoreduktase (UxuB) und Mannonate Dehydratase (UxuA) katalysiert. Weitere Experimente verdeutlichten, dass osmotischer Stress die Expression der Gene uxaCA, uxaB und uxuAB verminderte. Darüber hinaus zeigten kduID defiziente E. coli Mutanten in Gegenwart von Galakturonat oder Glukuronat und durch Saccharose ausgelösten osmotischen Stress eine Verlangsamung des Wachstums. Das deutet darauf hin, dass KduI und KduD die durch osmotischen Stress bedingten Funktionseinschränkungen der regulären hexuronatabbauenden Enzyme kompensieren. Die beobachtete Bildung von intrazellulären Hexuronaten während des Laktosekatabolismus in vitro stellt eine Verbindung zu dem ursprünglichen Tierexperiment her und deutet darauf hin, dass der Ernährungsfaktor Laktose die Verfügbarkeit von Hexuronat für intestinale E. coli beeinflusst. Diese Studie weist somit den Einfluss von osmotischem Stress auf die Expression von OxyR abhängigen Genen, die für Stressantwortproteine sowie für metabolische Enzymen kodieren, in E. coli nach. Durch Nahrungsfaktoren entstandener osmotischer Stress stellt demnach einen entscheidenden Faktor für die bakterielle Kolonisation des Darmes dar.

Pienarūgščių bakterijų paieška ir jų identifikavimas migruojančių didžiųjų ančių (Anas platyrhynchos) žarnyne naudojant dalinių 16S rRNR geno sekų analizę ir kultivavimu paremtus metodus Klaidas VARNA Vilniaus Universiteto Ekologijos Institutas, Hidrobiontų Ekologijos ir Fiziologijos Laboratorija bei Populiacinės Genetikos Laboratorija, Akademijos-2, Vilnius-21, 08412, Lietuva. Šiame tyrime pavasarinių ir rudeninių didžiųjų ančių (Anas platyrhynchos) migrantų iš Nemuno deltos virškinamojo trakto pieno rūgšties bakterijų įvairovė buvo ištirta naudojant molekulinius metodus (polimerazės grandininės reakcijos amplifikacija ir dalinių 16S rRNR geno sekų sekvenavimas) ir kultivavimu paremtus metodus. Migruojančių didžiųjų ančių (Anas platyrhynchos) pieno rūgšties bakterijų paieška buvo atlikta pirmą kartą. Rudeniniai didžiųjų ančių migrantai plonojo žarnyno sienelėse (1.2×107 iki 2.1×107 k.f.v./g) ir jų turinyje (nuo 3.4×107 iki 1.1×108 k.f.v./g) turi didesnį pieno rūgšties bakterijų skaičių nei pavasariniai migrantai (atitinkamai nuo 3.2×106 iki 4.8×106 k.f.v./g ir nuo 1.0×107 iki 2.2×107 k.f.v./g). Tiek rudeninių tiek ir pavasarinių didžiųjų ančių migrantų plonojo žarnyno sienelėse ir jų turinyje dominavo kokinės pieno rūgšties bakterijų formos (atitinkamai 65% ir 83.5% bei 81.4% ir 91.6%), o lazdelių buvo mažiau (atitinkamai 35% ir 16.5% bei 18.6% ir 8.4%). Manoma, kad minėtus skirtumus įtakoja keli veiksniai: ilgai trunkanti migracija, perėjimo periodas, skirtingas maistas ir... [toliau žr. visą tekstą] / Identification of lactic acid bacteria in the migrant mallard ducks Anas platyrhynchos intestinal tract by partial 16S rRNA gene sequence analysis and using culture-based techniques Klaidas VARNA Institute of Ecology of Vilnius University, Laboratory of Hydrobionts Ecology and Physiology, Laboratory of Population Genetics, Akademijos-2, Vilnius-21, 08412, Lithuania. In this study the lactic acid bacteria diversity of the intestinal tract content of the vernal and autumnal migrant mallard ducks (Anas platyrhynchos) from Nemuno delta has been investigated by molecular methods: polymerase chain reaction amplification and sequencing of partial 16S rRNA genes and using culture-based techniques. The investigation of the lactic acid bacteria of the migrant mallard ducks has been performed the first time. Autumnal migrant mallard ducks in the small intestine walls (from 1.2×107 until 2.1×107 c.f.u./g) and in their content (from 3.4×107 until 1.1×108 c.f.u./g have the greatest number of the lactic acid bacteria then vernal migrants (respectively from 3.2×106 until 4.8×106 c.f.u./g and from 1.0×107 until 2.2×107 c.f.u./g). In the small intestine walls and in their content of the autumnal and vernal migrant mallard ducks, dominated cocci-shaped lactic acid bacteria (respectively 65% and 83.5%, 81.4% and 91.6%), whereas rod-shaped was under (respectively 35% and 16.5%, 18.6% and 8.4%). Supposedly, that these defferences determine some factors: a long migration, period of incubate... [to full text]

The overall goal of this research is to understand roles of gut microbiota metabolites and adipocyte transcription factor (TF) network in health and disease by developing systematic analysis methods. As microbiota can perform diverse biotransformation reactions, the spectrum of metabolites present in the gastrointestinal (GI) tract is extremely complex but only a handful of bioactive microbiota metabolites have been identified. We developed a metabolomics workflow that integrates in silico discovery with targeted mass spectrometry. A computational pathway analysis where microbiota metabolisms are modeled as a single metabolic network is utilized to predict a focused set of targets for multiple reaction monitoring (MRM) analysis. We validated our methodology by predicting, quantifying in murine cecum and feces and characterizing tryptophan (TRP)-derived metabolites as ligands for the aryl hydrocarbon receptor. The adipocyte process of lipid droplet accumulation and differentiation is regulated by multiple TFs that function together in a network. Although individual TF activation is previously reported, construction of an integrated network has been limited due to different measurement conditions. We developed an integrated network model of key TFs - PPAR, C/EBP, CREB, NFAT, FoxO1, and SREBP-1c - underlying adipocyte differentiation. A hypothetic model was determined based on literature, and stochastic simulation algorithm (SSA) was applied to simulate TF dynamics. TF activation profiles at different stages of differentiation were measured using 3T3-L1 reporter cell lines where binding of a TF to its DNA binding element drives expression of the Gaussia luciferase gene. Reaction trajectories calculated by SSA showed good agreement with experimental measurement. The TF model was further validated by perturbing dynamics of CREB using forskolin, and comparing the predicted response with experimental data. We studied the molecular recognition mechanism underlying anti-inflammatory function of a bacterial metabolite, indole in DC2.4 cells. The indole treatment attenuated the fraction of cells that were producing the pro-inflammatory cytokine, TNFα and knockdown of nuclear receptor related 1 (Nurr1; NR4A2) resulted in less indole-derived suppression of TNFα production. The first discovery of NR4A2 as a molecular mediator of the endogenous metabolite, indole is expected to provide a new strategy for treatment of inflammatory disorders.

Vitamin D may have immunomodulatory effects in the intestine. Our objective was to determine if exposure to vitamin D mitigates intestinal inflammation in IL-10 KO mice. Mice were randomized to a diet containing 25 IU (low) or 5000 IU (high) of vitamin D/kg of diet in utero and offspring were maintained on the same diet or switched to the other diet at weaning. Fecal samples were collected at 3 months of age. Vitamin D did not affect intestinal inflammation in male and female mice and did not affect KC cytokine concentration or regulate colonic gene expression in male mice. Vitamin D modulated the gut microbiota in a sex-specific manner and depending on timing of exposure. Females in the HH group had significantly higher fecal counts of C. coccoides than the other vitamin D interventions. Therefore, vitamin D may favourably modulate microbiota composition without attenuating inflammation.