Resumo: Experimento 1: Foram avaliados os efeitos da substituição do milho pelo sorgo na ração para frangos de corte sobre o desempenho, o rendimento de carcaça e partes, a morfometria (densidade de vilos, altura dos vilos, profundidade das criptas, número de células caliciformes e índice mitótico nas criptas) e a integridade da mucosa do duodeno, jejuno e íleo, e a atividade das enzimas de membrana (aminopeptidase, fosfatase alcalina e maltase) da mucosa do jejuno. Foram utilizados 792 pintainhos de um dia machos, Cobb-500, distribuídos ao acaso em quatro tratamentos (0, 50, 75 ou 100% de substituição do milho pelo sorgo do 1º ao 42º dia) e seis repetições. No 7º, 21º e 42º dia o peso dos frangos e as sobras das rações foram aferidas, e foram obtidas amostras do intestino delgado de um frango por repetição. Experimento 2: Foi avaliado o efeito da substituição total do milho pelo sorgo sobre as Enterobactérias, Lactobacillus spp, Clostridium perfringens (Log10 UFC/g), a viscosidade e o pH do conteúdo ileal. Cem pintainhos foram distribuídos em dois grupos e alimentados com rações à base de milho ou sorgo do 1º ao 42º dia de idade. Concluiu-se desses experimentos que a substituição do milho da ração por sorgo, na fase inicial (1 a 21 dias), não altera o desempenho e a função da mucosa do intestino delgado dos frangos. A substituição parcial do milho pelo sorgo (50 ou 75%) durante a fase total de criação (1 a 42 dias) melhora a conversão alimentar dos frangos. A substituição total (100%), até os 42 dias, prejudica a estrutura dos vilos do duodeno e jejuno, mas, diminui a colonização por Clostridium perfringens no íleo e a viscosidade do conteúdo ileal. A substituição de 75 ou 100% até os 42 dias diminui a atividade de aminopeptidase e maltase. O rendimento de carcaça e partes, a atividade da fosfatase alcalina intestinal e as populações ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Experiment 1: The effects of substitution of corn by sorghum in diets for broiler chickens on performance, carcass and parts (breast and thigh+drumstick), morphology (density of villi, villous height, depth crypts, number of goblet cells and mitotic index in the crypts) and integrity (score of epithelial loss) of the duodenum, jejunum and ileum mucosa, and the activity of membrane enzymes (aminopeptidase, intestinal alkaline phosphatase, and maltase) of the jejunum. We used 792 day-old chicks male Cobb-500, were randomly assigned to four treatments (0, 50, 75 or 100% replacement of corn by sorghum 1 to 42 days) and six replications. At 7, 21 and 42 days the weight of the chickens and the remains of the diets were measured, and samples were collected from the small intestine of a chicken for replication. Experiment 2: The effect of total substitution of corn by sorghum on the counts of Enterobacteriaceae, Lactobacillus spp and Clostridium perfringens, viscosity and pH of ileal contents. One hundred chicks were divided into two groups and fed diets based on corn or sorghum, 1 to 42 days of age. From the results of these experiments it was concluded that the substitution of corn by sorghum in the initial phase (1 to 21 days) does not affect the performance and function of small intestinal mucosa of chickens. The partial substitution of corn by sorghum (50 or 75%) during the total period (1 to 42 days) seems to improve feed conversion of chickens. Total substitution (100%), up to 42 days, affect the structure of the villi of the duodenum and jejunum, but reduced colonization by Clostridium perfringens in the ileum and the viscosity of ileal contents. The replacement of 75 or 100% up to 42 days reduces the activity of aminopeptidase and maltase. The carcass and parts, the activity of intestinal alkaline phosphatase and the count of Enterobacteriaceae and Lactobacillus spp, are not affected by treatments / Orientador: Marcos Macari / Coorientador: Renato Luis Furlan / Banca: Alex Maiorka / Banca: Alice Eiko Murakami / Banca: Isabel Cristina Boleli / Banca: João Martins Pizauro Junior / Doutor

Dans le contexte du réchauffement climatique, les récifs coralliens subissent des stress thermiques de plus en plus fréquents et intenses. Dans le but de mieux comprendre les mécanismes de la thermo­tolérance des coraux, j’ai développé une approche intégrative sur l’holobionte corallien (méta­organisme composé de l’hôte corallien, son algue symbiotique etson microbiote). Pour cela, j’ai réalisé une expérience de stress thermique écologiquement réaliste sur une espèce de corail, Pocillopora damicornis. Cette espèce étant présente dans l’ensemble de l’Indo­Pacifique, j’ai pu comparer la réponse de deux populations dont la thermotolérance est différente puisqu’elles sont soumises à des régimes thermiques contrastés. J’ai analysé, pour chacune d’entre­elles, la réponse de l’hôte corallien (par RNAseq), ainsi que la structure et les changements au niveau des microbiotes algaux et bactériens (par métabarcoding). Les résultats obtenus montrent qu’alors que la structure du microbiote n’est pas influencée par le stress, le corail y répond de façon très différente selon la population étudiée. La population issue d’un environnement plus fluctuant met en place une réponse plus efficace et plus plastique, probablement grâce à l’intervention de mécanismes épigénétiques. Une autre étude réalisée sur différentes populations de P. damicornis dans le cadre de cette thèse montre que la composition du microbiote est influencée par le génome de l’hôte ainsi que par le régime thermique. Un des clades de l’algue symbiotique connu pour améliorer la thermo­ tolérance de l’hôte corallien semble plus sensible aux basses températures que les autres. / In the context of global warming, coral reefs are experiencing thermal stresses which are becoming more frequent and intense. In order to get a better understanding of the mechanisms of coral thermo­tolerance, I developed an integrative approach on the coral holobiont (meta­ organism composed of the coral host, its symbiotic algae and microbiota). For this, I performed an ecologically realistic thermal stress experiment on a coral species, Pocillopora damicornis. This species is widespread in the Indo­Pacific area. I compared the response of two populations whose thermotolerance is different since they are subjected to contrasting thermal regimes. I analyzed, for each of them, the response of the coral host (by RNAseq), as well as the structure and changes in the algal and bacterial microbiota (by metabarcoding). The results show that,while the structure of the microbiota is not influenced by stress, coral responds very differently depending on the population studied. The population from a more fluctuating environment displays a more effective and more plastic response, probably thanks to the involvement of epigenetic mechanisms. Another study carried out on different populations of P. damicornisshowed that the composition of the microbiota is influenced by the host genome and the thermal regime. One of the clades of the symbiotic algae, known to improve the heat­tolerance of the coral host, appears more sensitive to low temperatures than the others.

Notre équipe a précédemment rapporté que l'utilisation d'un traitement d'induction lympho-déplétant [les globulines anti-lymphocytaires polyclonales (GALP)], peut entrainer une lymphopénie T CD4 persistante chez certains transplantés rénaux. Celle-ci est associée à certaines anomalies biologiques telles que la présence d'un syndrome inflammatoire chronique. Ce travail de thèse s'intéresse aux facteurs impliqués dans l'induction de ces anomalies puisqu'elles sont associées à une augmentation de l'incidence d'infections, de maladies cardiovasculaires et de décès, habituellement retrouvés chez les personnes âgées. Nous avons montré que les GALP entrainent une diminution de la fonction thymique et une expansion de lymphocytes T à un stade avancé de différenciation pouvant traduire une immunosénescence prématurée. Par ailleurs, une rupture de la barrière intestinale semble favoriser la translocation bactérienne digestive et l'activation d'une inflammation chronique observée en transplantation, via les lipopolysaccharides libérés dans la circulation périphérique. La composition du rnicrobiote intestinal pourrait jouer un rôle dans l'initiation, le maintien et la sévérité de l'inflammation. Nous avons observé des modifications du microbiote après transplantation et après l' antibioprophylaxie utilisée en transplantation. Les mécanismes à l'origine de toutes ces observations restent à élucider mais ce travail permet d'améliorer la compréhension des facteurs impliqués dans le développement de l'immunosénescence et de l'inflammation chronique en transplantation rénale, ouvrant potentiellement la voie à d'intéressantes perspectives thérapeutiques. / We bave previously described that polyclonal anti-lymphocytic globulins (GALP) may contribute to prolonged CD4 T­cell lymphopenia in some renal transplant recipients, associated with some biological abnormalities, such as a chronic inflammatory syndrome. Our work focuses on the factors involved in the induction of tbese abnormalities and susceptible to increase the incidence of infections, cardiovascular diseases and deatb, comparable to the incidence observed in the elderly. We showed that GALP are implicated in the decrease in thymie output and the expansion ofT cells at an advanced stage of differentiation. Both are hallmarks of premature immune senescence. Moreover, the dysfunction of the gut epithelial barrier is responsible for gut bacterial translocation (GBT) and the activation of chronic inflammation observed in chronic kidney disease as well as in renal transplant recipients. The composition of the intestinal microbiota may play a role in the initiation, maintenance and severity of GBT and systernic inflammation. We reported the existence of a dysbiosis a.fier transplantation. The mechanisms involved remain to be elucidated, yet, this work contributes to the understanding of the potential factors involved. in the progression of immune senescence and the persistence of chronic inflammation after kidney transplantation paving the way to new fields of therapeutic research in transplantation

Submitted by (edna.saturno@ufrpe.br) on 2016-07-28T13:32:52Z No. of bitstreams: 1 Andrea Paiva Botelho Lapenda Moura.pdf: 326144 bytes, checksum: 620eeb1d70babd2fa43af8e1560d7095 (MD5) / Made available in DSpace on 2016-07-28T13:32:52Z (GMT). No. of bitstreams: 1 Andrea Paiva Botelho Lapenda Moura.pdf: 326144 bytes, checksum: 620eeb1d70babd2fa43af8e1560d7095 (MD5) Previous issue date: 2006-02-20 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Evaluation of microbiological quality of chilled and in natural goat meat sold in public/private markets and supermarkets of Recife concerning Staphylococcus aureus counting, total and thermotolerant coliforms,identification and typing of Salmonella spp, was the objective of this study. Antimicrobial sensibility profile in vitro of Staphylococcus aureus and Salmonella spp samples and the correlation between the simultaneous presence of faecal coliforms and Salmonella spp. were also performed. The study was carried out at six public/private markets and nine supermarkets of Recife, which were selected according to the administrative division of Local Authority Healthy General Office in six sanitary districts. A total of 24 samples of goat meat, 14 proceeded from public/private markets in natura and 10 chilled ones from supermarkets. Samples were processed using methodologies recommended by the Agriculture, Pecuary and Provision Ministry. Results demonstrated that 11 samples (45,83%) presented positive coagulasis staphylococcus (SCP) varying from 6.7 x 103 to 1.4 x 106 UFC/g, corresponding to 27 isolated from a total of 89. In total coliforms analyses, five samples (20.83%) presented satisfactory sanitary conditions and 19 (79.16%) had countings varying from 4.3 x 103 to 3.7 x 107, thermotolerants coliforms were detected in 15 (62.5%), which countings varied from 2 x 104 to 2.5 x 107 UFC/g and nine samples (37.5%) presented satisfactory sanitary conditions. Presence of Salmonella spp., was confirmed at seven samples (29.17%) in which eight sorovares were typed: four (50%) Salmonella enterica subsp houtenae (O:53), two (25%) S. Anatum, one (12.50%) S.Rubislaw and one (12, 50%) S. Derby. No correlation was observed among coliforms and Salmonella presure. Antimicrobial profile sensibility showed that S. aureus were sensitive to norfloxacin and vancomicin (100%), tetraciclin and sulpha + trimetoprim (96.30%) and oxacilin (87.50%) and 100 % of Salmonella spp. samples were sensitive norfloxacin, 75% sulpha + trimetoprim and 62.5% tetraciclin. It is concluded that goat meat sold at markets and supermarkets of Recife presented undesirable microbiological patterns emphasizing the importance of a strong supervision at the productive goat meat chain as well as a revision of the Resolution of Collective Management from the National Agency of Sanitary Vigilance, (RDC, n°12/2001) which does not establish microbiological patterns for the coliforms and Staphylococcus spp countings in chilled and in natura goat meat. / Objetivou-se com este estudo avaliar a qualidade microbiológica da carne caprina in natura e resfriada, comercializada em mercados públicos/privados e supermercados na Cidade do Recife, quanto a contagem de Staphylococcus aureus, coliformes totais e termotolerantes, e identificação e tipificação de Salmonella spp. Realizou-se, também, o perfil de sensibilidade antimicrobiana in vitro de amostras de Staphylococcus aureus e Salmonella spp e a correlação entre a presença simultânea de coliformes fecais e Salmonella spp. O estudo foi realizado em seis mercados públicos/privados e nove supermercados da Cidade do Recife, selecionados seguindo a divisão administrativa da Secretaria de Saúde do Município em seis Distritos Sanitários. Foram analisadas 24 amostras de carne caprina, sendo 14 in natura procedentes de mercados públicos/privados e 10 resfriadas de supermercados. As amostras foram processadas utilizando metodologias preconizadas pelo Ministério da Agricultura, Pecuária e Abastecimento. Os resultados demonstraram que 11 (45,83%) amostras apresentaram contagens de estafilococos coagulase positiva (SCP) variando de 6,7 x 103 a 1,4 x 106 UFC/g, correspondendo a 27 isolados de um total de 89. Para coliformes totais, cinco (20,83%) amostras encontravam-se em condições sanitárias satisfatórias e 19 (79,16%) apresentaram contagens variando de 4,3 x 103 a 3,7 x 107; e para termotolerantes 15 (62,5%) apresentaram contagens variando de 1,2 x 104 a 2,5 x 107 UFC/g e nove (37,5%) encontravam-se em condições sanitárias satisfatórias. Foram confirmadas em sete (29,17%) amostras a presença de Salmonella spp., nas quais foram tipificadas oito sorovares: quatro (50,00%) Salmonella enterica subsp houtenae (O:53), duas (25,00%) S. Anatum, uma (12,50%) S.Rubislaw, uma (12,50%) S. Derby. Não se observou correlação entre as bactérias estudadas. O perfil de sensibilidade antimicrobiana demonstrou que os antibióticos mais indicados para o tratamento de S. aureus foram norfloxacina e vancomicina (100%), tetraciclina e sulfa + trimetoprim (96,30%) e oxacilina (87,50%) e para Salmonella spp. 100% das amostras foram sensíveis à norfloxacina, 75,00% à sulfa + trimetoprim e 62,5% para tetraciclina. Conclui-se que a carne caprina comercializada nos mercados e supermercados da Cidade do Recife apresentou padrões microbiológicos indesejáveis ressaltando a importância da necessidade de uma maior fiscalização na cadeia produtiva da carne caprina bem como rever a Resolução da Diretoria Colegiada da Agência Nacional de Vigilância Sanitária (RDC, n°12/2001) que não estabelece padrões microbiológicas para a contagem de coliformes termotolerantes e Staphylococcus spp. em carne caprina in natura e resfriada.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-06-05T14:54:01Z No. of bitstreams: 1 2010 - Samuel_Ribeiro_Passos.pdf: 16768295 bytes, checksum: 38c2614ad26085e9a101652551af84b5 (MD5) / Made available in DSpace on 2017-06-05T14:54:01Z (GMT). No. of bitstreams: 1 2010 - Samuel_Ribeiro_Passos.pdf: 16768295 bytes, checksum: 38c2614ad26085e9a101652551af84b5 (MD5) Previous issue date: 2010-02-23 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior, CAPES, Brasil. / The increasing demand for biological processes alternative, environmentally friendly and efficient in converting lignocellulosic material, expanding their application potential for agribusiness, motivates researches worldwide. Thus, organisms isolated in nature, in specific ecosystems, become increasingly important because of their physiological and metabolic diversity, which gives them a great potential in the development of biotechnological processes of interest to society. The aim of this study was to assess the microbial community associated with the intestinal tract of millipede Trigoniulus corallinus and bioprospecting for microorganisms with cellulolytic capacity. The millipedes were collected and incubated with litter in diets of grass (Paspalum notatum) and ?sabia? (Mimosa caesalpinifolia). Sampling occurred at 15, 30, 45, and 75 days of incubation. The intestinal tract of five individuals was removed, sectioned the posterior third, processed and stored in ultrasound. DNA from microbes associated with the intestinal tract, litter and coprolite was extracted, and DGGE analysis using 16S rDNA, DGGE group actinomycetes, and it was evaluated the presence of nifH genes. The 16s gene analysis by DGGE revealed a microbial diversity conditioned by the diet offered to 45 days. After this period, this effect was no longer visible. The community associated with coprolites and the type of litter was distributed in separate clusters of samples from the intestinal tract. This effect was not observed in the community assessment of actinomycetes, where the big difference for division of groups was the diet. The animals fed on grass litter showed a diverse community, and they were not influenced by time or compartmentalization. The samples associated with litter and coprolites were 80% similar to samples from the intestinal tract. In millipedes fed with material form Mimosa caesalpinifolia, the result was different, the samples of litter and coprolites where 50% similar to the intestinal tract. All samples had nifH genes detected by polymerase chain reaction. Samples collected at 45 days were also inoculated in mineral minimum medium of Busnell-Hass added carboxymethyl-cellulose (CMC) as sole carbon source. Colonies were evaluated for their ability to breakdown cellulose enzyme and 15 had an index greater than 1. The isolate that showed the highest rate (3.65) was subjected to further analysis. The microscope observation suggested that this was not an isolated but a complex of microorganisms acting on the degradation of cellulose. There is evidence of BNF in the intestinal tract of the millipede and microorganisms proliferated in CMC through the proper amplification of nifH genes and proliferation in medium within nitrogen. The community of prokaryotes was influenced by the diet offered to the community up to 45 days, and the actinomycetes community was conditioned by the diet. It was possible to isolate microorganisms and complexes of microorganisms with cellulolytic capacity, with great potential in the search for environmentally friendly technologies in generating agrobioenergy. / A crescente demanda por processos biol?gicos alternativos, ambientalmente favor?veis e eficientes na transforma??o de material ligninocelul?sico, ampliando seu potencial de aplica??o agroindustrial, estimula pesquisas em todo o mundo. Assim, microrganismos isolados na natureza, em ecossistemas espec?ficos, tornam-se cada vez mais importantes pela sua diversidade metab?lica e fisiol?gica, que lhes confere grande potencialidade no desenvolvimento de processos biotecnol?gicos de interesse ? sociedade. O objetivo deste trabalho foi avaliar a comunidade microbiana associada ao trato intestinal do dipl?pode Trigoniulus corallinus e a bioprospec??o de microrganismos com capacidade celulol?tica. Os dipl?podes foram coletados e incubados em dietas com serrapilheira de grama batatais (Paspalum notatum) e sabi? (Mimosa caesalpinifolia). As amostragens aconteceram aos 15, 30, 45 e 75 dias de incuba??o. O trato intestinal de cinco indiv?duos foi removido e seccionado o ter?o posterior tratado em ultrasom e estocado. Procedeu-se a extra??o de DNA da microbiota associada ao trato intestinal, serrapilheira e copr?lito, com an?lise por DGGE utilizando o gene 16S rDNA, DGGE para grupo actinomicetos e avalia??o da presen?a de genes nifH. A an?lise do gene 16s por DGGE revelou diversidade microbiana condicionada pela dieta oferecida at? os 45 dias. Ap?s este per?odo o efeito n?o foi mais vis?vel. A comunidade associada aos copr?litos e ao tipo de serrapilheira distribui-se em grupamentos separados das amostras oriundas do trato intestinal. O mesmo n?o foi observado na avalia??o da comunidade de actinomicetos, onde o grande diferencial para divis?o de grupos foi a dieta. Os animais alimentados com serrapilheira de grama mostraram uma comunidade diversa e n?o influenciada pelo tempo ou compartimentaliza??o. As amostras associadas ? serrapilheira e aos copr?litos foram 80% similares ?s do trato intestinal. Nos dipl?podes alimentados com sabi?, o resultado foi diferente, sendo as amostras de serrapilheira e copr?litos 50% similares ?s do trato intestinal. Todas as amostragens tiveram genes nifH detectados via PCR. Amostras coletadas aos 45 dias foram tamb?m inoculadas em meio mineral m?nimo de Busnell-Hass adicionado de carboxi-metil-celulose (CMC) como ?nica fonte de carbono. Os microrganismos isolados foram avaliados quanto ? capacidade de degrada??o de celulose e 15 apresentaram ?ndice enzim?tico maior que 1. O isolado com o maior ?ndice (3,65) foi alvo de outras an?lises. A visualiza??o em microsc?pio sugeriu que n?o se tratava de um isolado e sim de um complexo de microrganismos atuando na degrada??o da celulose. H? evidencias de FBN no trato intestinal do dipl?pode e microrganismos proliferados em meio CMC pela boa amplifica??o de genes nifH e prolifera??o em meio com aus?ncia de nitrog?nio. A comunidade de procariotos foi influenciada pela dieta oferecida at? os 45 dias e a comunidade de actinomicetos foi condicionada em fun??o da dieta. Foram isolados microrganismos e complexos de microrganismos com capacidade celulol?tica, com grande potencial para a busca de tecnologias ambientalmente sustent?veis na gera??o de agrobioenergia.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-09-26T14:39:58Z No. of bitstreams: 1 joseeugenioriosriccijunior.pdf: 958378 bytes, checksum: f20499edf79931ac9fe901f9233cd200 (MD5) / Approved for entry into archive by Diamantino Mayra (mayra.diamantino@ufjf.edu.br) on 2016-09-26T20:34:06Z (GMT) No. of bitstreams: 1 joseeugenioriosriccijunior.pdf: 958378 bytes, checksum: f20499edf79931ac9fe901f9233cd200 (MD5) / Made available in DSpace on 2016-09-26T20:34:06Z (GMT). No. of bitstreams: 1 joseeugenioriosriccijunior.pdf: 958378 bytes, checksum: f20499edf79931ac9fe901f9233cd200 (MD5) Previous issue date: 2016-08-12 / O supercrescimento bacteriano do intestino delgado (SCBID) é definido como um aumento no número e/ou alteração no tipo de bactérias no intestino delgado. Na sua patogênese incluem dano à válvula ileocecal e anormalidades anatômicas, comuns na doença de Crohn (DC). O presente estudo tem como objetivo estudar a prevalência e preditores de SCBID em pacientes com DC, assim como avaliar a relação entre SCBID e inflamação sistêmica e/ou intestinal. Neste estudo transversal, entre Junho de 2013 e Janeiro de 2015, 92 pacientes com DC e 97 controles com queixas gastrointestinais não crônicas foram avaliados quanto à presença de SCBID usando o teste respiratório (TR) com hidrogênio e metano exalados. Regressão logística multivariada foi realizada para investigar a potencial associação entre SCBID com dados demográficos, características da doença, marcadores sistêmicos de inflamação (proteína C reativa - PCR - e velocidade de hemossedimentação de eritrócitos - VHS), e biomarcador fecal de inflamação intestinal (calprotectina fecal - CF). A taxa de SCBID foi significativamente maior em pacientes com DC do que nos controles (32,6% vs. 12,4%, respectivamente; p = 0,0008). Os pacientes com e sem SCBID foram semelhantes de acordo com os dados demográficos, marcadores inflamatórios sistêmicos e características da doença, exceto o fenótipo estenosante, mais comum nos pacientes com DC positivos para SCBID (43,3% vs. 19,3%; p = 0,015). Notavelmente, a concentração de CF foi significativamente mais elevada em pacientes positivos para SCBID (mediana de 485,8 vs.132,7 ug/g; p = 0,004). Os pacientes que apresentaram aumento da CF e doença estenosante tiveram um odds de 9,43 (IC de 95%, 3,04-11,31; p <0,0001) e 3,83 (95% CI, 1,54-6,75; p = 0,025), respectivamente, para o diagnóstico de SCBID. Em pacientes com DC, o SCBID é uma condição altamente prevalente. O fenótipo estenosante e o aumento da concentração de CF foram fortemente e independentemente associados com a presença de SCBID. O diagnóstico de SCBID seguido de tratamento direcionado é recomendado em pacientes com DC, especialmente no cenário de fenótipo estenosante e/ou na presença concomitante de inflamação intestinal. / Introduction: The small intestine bacterial overgrowth (SIBO) is defined as an increase in the number and/or change in the type of bacteria in the small intestine. In its pathogenesis it is important the damage on the ileocecal valve and anatomical abnormalities, both common in Crohn's disease (CD). The aim of this study was to determine the prevalence and predictors of SIBO in CD patients as well as to assess the relationship between SIBO and systemic and/or intestinal inflammation. In this cross-sectional study, between June 2013 and January 2015, 92 CD patients and 97 controls with non-chronic gastrointestinal complaints were assessed for presence of SIBO using the H2/CH4 glucose breath test. Multivariate logistic regression was performed to investigate the potential association between SIBO and demographic, disease-related data, systemic markers of inflammation (C-reactive protein and erythrocyte sedimentation rate), and biomarker of intestinal inflammation (fecal calprotectin concentration - FCC). The SIBO rate was significantly higher in CD patients than in the controls (32.6% vs. 12.4%, respectively, P=0.0008). Patients with and without SIBO were comparable according to demographics, systemic inflammatory biomarkers, and disease characteristics, except to the stricturing phenotype more common in the SIBO-positive CD patients (43.3% vs. 19.3%, P=0.015). Notably, FCC was significantly higher in SIBO-positive patients (median of 485.8 vs.132.7 μg/g; P = 0.004). Patients presenting increased FCC and stricturing disease had an odds of 9.43 (95% CI, 3.04-11.31; P <0.0001) and 3.83 (95% CI, 1.54-6.75; P=0.025) respectively, for SIBO diagnosis. Conclusions: In CD patients, SIBO is a highly prevalent condition. Stricturing phenotype and increased FCC were strongly and independently associated with the presence of SIBO. SIBO diagnostic work-up followed by directed treatment is recommended in CD patients, especially if stricturing disease or concurrent intestinal inflammation is present.

Made available in DSpace on 2014-08-20T13:32:49Z (GMT). No. of bitstreams: 1 tese_erico_kunde.pdf: 287917 bytes, checksum: c139b1164d4ea5a2964a48d21cf91781 (MD5) Previous issue date: 2007-02-28 / Deep litter systems (DLS) have lower facility cost and less environmental impact than conventional swine production systems, but the animal thermal comfort may not be ideal, during warm seasons. This thesis studied the effect of the use of litters having different depths on indicators of environmental comfort, animal growth performance and physical, chemical and microbiological characteristics of the litter. Three treatments were compared: solid concrete floor (control); litter of rice husk with depth of 0.25 (L25) and 0.50 m (L50). The first liter was used in two lots and replaced by a second litter used in other two lots. The environmental conditions were determined by the relative humidity of the air (RH), atmospheric temperature (AT) and litter temperature at the center of the pen, both in the surface (TSF) and at half of the depth (THD). Feed intake, weight gain and feed conversion for the pigs raised on DLS were also estimated. Concentrations of thermophilic and mesophilic bacteria, fungi and actinomycetes were determined by the most probable number method. TSF was lowest in the control group (P < 0.05), but it did not differ between C25 and C50 (P > 0.05). TSF was higher for new than for used litters and for the first than for the second litters (P < 0.05). The highest levels of N, P and K found in the L25 indicate that its compost has greater agronomical values. The concentration of mesophilic bacteria was higher in L50 than in L25 (P < 0.05). Although no statistical comparison was performed for growth performance parameters, feed conversion was similar for pigs in the control and DLS groups, with an apparent advantage for L25. This thesis also studied the effect of the addition of inoculums, in a pilot scale, on litters similar to those used in DLS, on the parameters mentioned above. The experimental units were boxes having area equal to 1 m2., on which litter of rice husk was added at the depths of 0.25 (L25) and 0.50 m (L50). On a daily basis, 6.4 l of swine dejects were added to the boxes, which consisted of three treatments: control without inoculums (T1); inoculation of 250 g of Bacillus cereus var. tyoii with 8,4 x 107 UFC/g (T2); and inoculation of 250 g of EnziLimp with 8,4 x 107 UFC/g (T3). Concentration of mesophilic and thermophilic bacteria, fungi and actinomycetes were determined and the chemical characteristics of the litter were evaluated. The addition of inoculums allowed higher concentration of thermophilic bacteria than in the control group (P < 0.05), so it would not be recommended for DLS. There was a higher concentration of thermophilic bacteria and fungi in the first lot of L50 (P < 0.05). Increased N level had a negative association with the concentration of all the thermophilic microbial populations (P < 0.05). Therefore, L25 can be recommended as a feasible option for DLS because it is associated with reduced concentration of thermophilic microbial populations in the litter, which leads to better thermal comfort for the pigs, without negative effects for growth performance, also generating compost having high agronomical value. / Em comparação com sistemas convencionais de criação de suínos, o sistema de produção sobre cama (SPC) utiliza edificações de menor custo e menor impacto ambiental, mas pode prejudicar o conforto térmico dos animais, em climas quentes. Esta tese estudou os efeitos das camas usadas para SPC, com diferentes profundidades, sobre indicadores de condicionamento ambiental da edificação, desempenho de crescimento dos animais, e características físicas, químicas e microbiológicas das camas. Três tratamentos foram comparados: piso de concreto (controle) e camas de casca de arroz com profundidade de 0.50 (C50) e 0.25 m (C25). A primeira cama foi usada em duas repetições e substituída por uma segunda cama usada em outras duas. A condição ambiental foi determinada através da umidade relativa do ar (UR) e das temperaturas atmosférica (TA) e no centro da baia, tanto na superfície (TCS), como na metade da profundidade (TCI). Também foram estimados o consumo de alimento, o ganho de peso e a conversão alimentar dos animais. Através de NMP, determinaram-se as concentrações de bactérias, fungos e actinomicetos, mesófilos e termófilos. A TCS foi mais baixa para o controle (P < 0,05), mas sem diferença entre C25 e C50 (P > 0,05). A TCS foi maior nas camas novas do que nas usadas e para as primeiras do que nas segundas camas (P < 0,05). Os maiores teores de N, P e K presentes na C25 indicaram que o composto produzido nesta profundidade possui melhor valor agronômico. A concentração de bactérias termófilas foi maior na C50 do que na C25 (P < 0,05). Ainda que não tenham sido feitas comparações estatísticas, a conversão alimentar foi similar para os animais no grupo controle e no SPC, com aparente benefício na C25. Esta tese também estudou o efeito da adição de inóculos, em escala piloto, sobre camas similares as usadas no SPC, sobre os parâmetros mencionados acima, em experimento realizado em uma granja comercial. As unidades experimentais foram caixas com 1 m2 de área, nas quais foi adicionada cama de casca de arroz, em profundidades de 0,25 (C25) e 0,50 m (C50). Diariamente, foram adicionados 6,4 l de dejetos por caixa, formando três tratamentos: controle sem inoculo (T1); inoculação de 250 g de Bacillus cereus var. tyoii com 8,4 x 107 UFC/g (T2); e inoculação de 250 g de EnziLimp com 8,4 x 107 UFC/g (T3). Foram determinadas as concentrações de bactérias, fungos e actinomicetos, mesófilos e termófilos e analisadas as características químicas das camas. A adição dos inóculos propiciou uma maior concentração de bactérias termófilas (P < 0,05), em relação ao controle, não sendo recomendável para animais em crescimento e terminação. Houve maior concentração de bactérias e fungos termófilos na primeira repetição da C50 (P < 0,05). A elevação do teor de N influenciou negativamente todas as concentrações microbianas termófilas (P < 0,05). Em conclusão, a C25 é uma opção viável para SPC, por apresentar um maior valor agronômico e possibilitar uma melhor conversão alimentar dos animais quando comparada com a C50.

Les plantes vivent en association avec une grande diversité de microorganismes qui forment son microbiota. Ce microbiote fournit des fonctions clés qui influencent tous les aspects de la vie d'une plante, de l'établissement à la croissance jusqu'à la production. Cette thèse a pour intention de déterminer les règlent d'assemblage du microbiote et ses conséquences pour le phénotypel l'adaptation et l'évolution des plantes. Pour atteindre cet objectif nous avont utilisé différentes approches expérimentales comprenant des plantes clonales comme organismes modèles ainsi que des mésocosmes prairiaux pour analyses à l'échelle des communautés. Nos résultats ont démontré i) que les Champignons Mycohiziens à Arbuscules induisent d'important es variations phénotypiques pour les traits des plantes clonales impliqués dans l'exploration de l'espace et l'exploitation des ressources. Ces changements dépendent de l'identité des symbiontes et altèrent les capacités des plantes à développer des réponses plastiques à l'hétérogénéité environnementale. ii) Les plantes ont évolué un méchanisme permettant la transmission d'une partie de leur microbiote a leur descendance, assurant la qualité de leur habitat. iii) Le contexte spécifique des communautés de plantes est un facteur majeur structurant l'assemblage du microbiota des plantes à échelle locale. L'abondance de certaines espèces de plante dans le voisinage d'une plante cible augmente ou diminue la diversité de son microbiote, déterminant in fine ses performances. De manière générale, cette thèse démontre l'importance des organismes symbiotiques dans la compréhension de l'adaptation et de l'évolution des plantes. / Plants live in association with a wide diversity of microorganisms forming the microbiota. The plant microbiota provides a variety of key functions that influence many aspects of plant's life comprising establishment, growth and reproduction. The present thesis aims at determining the assembly rules of the plant microbiota and its consequences for plant phenotype, adaptation and evolution. To fulfill this objective, we used different experimental approaches using either clonal plants as model organisms or grassland mesocosms for community-wide analyses. Our results demonstrated i) that Arbuscular Mycorrhizal Fungi induce important phenotypic variations in clonal plants traits involved in space exploration and resources exploitation. These changes depended on the identity of the symbionts and altered the plants ability to produce plastic responses to environmental heterogeneity. ii) Plants have evolved a mechanism allowing the transmission of a part of their microbiota to their progeny, ensuring thus their habitat quality. iii) The plant community context is a major factor structuring local plant microbiota assembly. Particular plant species identity in the neighborhood increase or decrease the microbiota diversity and ultimately determine the focal plant performance. This thesis overall demonstrates the importance of symbiotic microorganisms in the understanding of the plant adaptation and evolution. From the knowledges acquired we developed a novel understanding of symbiotic interactions in clonal plants by extending the holobiont theory to the meta-holobiont theory.

De nombreuses études suggèrent que le déclin des colonies d’abeilles domestiques (Apis mellifera) serait dû à l’action combinée de plusieurs facteurs de stress, et notamment des agents pathogènes et des pesticides. Nous avons précédemment démontré qu’une co-exposition des abeilles au parasite intestinal Nosema ceranae et à l'insecticide fipronil, administré chroniquement en doses sublétales, entraînait une forte augmentation de la mortalité des abeilles. De plus, des études suggèrent que l'infection par N. ceranae pourrait augmenter la capacité antioxydante des cellules intestinales de l'abeille. Nous nous sommes demandé si l'élévation du taux de mortalité dans un contexte d'infection, combiné à une intoxication au fipronil, pourrait être le résultat d'une production d'espèces réactives de l'oxygène (ERO). Nos résultats indiquent une diminution de la quantité des ERO, mais aussi de la quantité de protéines oxydées en présence de N. ceranae. Ceci pourrait être la résultante d’une augmentation des activités enzymatiques antioxydantes. Lorsque les abeilles ont été traitées avec les deux facteurs de stress (N. ceranae et fipronil), nous n’avons cependant pas mesuré d’augmentation des ERO, tandis que l’oxydation des protéines était significativement augmentée. Ainsi, la présence du parasite semble perturber la balance oxydative des cellules intestinales et pourrait augmenter la toxicité du fipronil. Des études complémentaires ont également été menées in vitro sur des cellules humaines HFF, infectées avec une autre espèce microsporidienne, Encephalitozoon cuniculi, et/ou exposées au fipronil. Les résultats ont montré que la présence du parasite limitait l’augmentation des ERO induite par le fipronil. De plus, des résultats préliminaires tendent à montrer une augmentation de l’activité métabolique des mitochondries dans les cellules infectées par le parasite. Enfin, dans le but de mieux comprendre le dialogue N. ceranae/abeille/microbiote intestinal, nous avons analysé par une approche de séquençage d’amplicons d’ADNr et d’ARNr 16S la composition et l’abondance des communautés microbiennes de l’intestin après infection et/ou intoxication chronique avec différents pesticides. N. ceranae semble perturber l’activité de plusieurs groupes bactériens, et la présence de pesticides accroît fortement ces perturbations. Ainsi, l’impact d’une co-exposition N. ceranae/pesticides sur le microbiote intestinal pourrait être l’un des éléments clés du déclin des colonies. / Many studies suggest that the observed decline of Apis mellifera honeybee colonies would be due to the combined action of multiple stressors, including both pathogens and pesticides. We previously demonstrated that the honeybee co-exposure to the gut parasite Nosema ceranae and the fipronil insecticide, administered chronically in sublethal doses, highly increased the bee mortality. Moreover, studies suggest that the infection by N. ceranae may increase the antioxidant capacity of the bee intestinal cells. We wondered whether the increase in mortality rate when infection is combined with fipronil intoxication could be the result of reactive oxygen species (ROS) production. Our results indicate that both the ROS amount and the concentration of oxidized proteins decreased upon infection. This could be the result of an increased antioxidant enzymatic activities. When bees were co-exposed to both stressors (N. ceranae and fipronil), we did not measured any increase in ROS level, but the amount of oxidized proteins was significantly increased. Thus, the presence of the parasite seems to disrupt the oxidative balance of the intestinal cells and could increase the toxicity of fipronil. Complementary studies were also conducted in vitro with human cells (HFF), infected with a different microsporidian species, Encephalitozoon cuniculi, and/or treated with fipronil. The results showed that the presence of the parasite reduced the increase in ROS induced by fipronil. In addition, preliminary results showed an increase in mitochondrial metabolic activity in cells infected with the parasite. Finally, in order to better understand the N. ceranae/honeybee/intestinal microbiota dialogue, we analysed the composition and the abundance of microbial communities in the gut after infection and/or intoxication with different pesticides using a next generation sequencing of both rDNA and rRNA 16S amplicons. N. ceranae seems to upset the activity of different groups of bacteria, and the presence of pesticides greatly increased these disturbances. Thus, the impact of N. ceranae/pesticide co-exposure on the intestinal microbiota may be one of the key elements in the decline of honey bee colonies.

Les interactions isopodes terrestres-Wolbachia féminisantes constituent un excellent modèle d'étude des interactions multipartites complexes. A ce jour, trois Wolbachia féminisantes, issues d'histoires évolutives différentes, ont été identifiées chez l'hôte Armadillidium vulgare. L'objectif de cette thèse est d'avoir une vue plus complète du microbiote d'A. vulgare et de l'impact des souches de Wolbachia sur cette communauté bactérienne. Dans ce but, des approches quantitative et métagénomique ont été combinées afin de caractériser le microbiote d'A.vulgare à plusieurs niveaux d'intégration: (i) dans des populations naturelles et des lignées contrôlées de laboratoire, (ii) au sein de différents tissus hôtes et (iii) en relation avec le statut d'infection par Wolbachia. Aucun microbiote coeur n'a été mis en évidence malgré une relative homogénéité des communautés symbiotiques dans les tissus de l'hôte. De plus, les bactéries environnementales avaient un impact important sur le microbiote symbiotique. Chez les animaux infectés, Wolbachia représente la bactérie dominante et le facteur majeur de la structuration de la communauté symbiotique. Nous avons également mis en évidence la présence d'un autre constituant majeur du microbiote dans tous les tissus de l'hôte: Candidatus Hepatoplasma crinochetorum, un symbiote facultatif réputé jusque-là pour être seulement associé aux glandes digestives de l'intestin. Afin d'éclairer les interactions potentielles entre hôte et ce symbiote relativement peu connu, la séquence du génome de Ca. H. crinochetorum a été obtenue. Une analyse préliminaire des interactions fonctionnelles des voies métaboliques impliquées dans la digestion de la cellulose nous a permis d'identifier des enzymes cellulolytiques spécifiques de l'hôte et du symbiote. Cette étude ouvre de nouvelles perspectives dans l'étude de la symbiose chez les isopodes. / In recent years, there has been a shift of focus in symbiosis studies, away from the traditional 'one host-one symbiont' concept towards a more holistic, community-based approach. This concept takes into account that a host is not only associated with one bacterium, but harbours and interacts with a diverse bacterial community, the microbiome. Terrestrial isopods represent an excellent model system for the understanding of complex multipartite symbioses due to their well-characterised association with feminizing Wolbachia bacteria. To date, three different feminizing Wolbachia strains have been identified in Armadillidium vulgare, presumably representing different host-symbiont co-evolutionary histories. The aim of this PhD was to get a more complete picture of the terrestrial isopod microbiome and the role of Wolbachia within the bacterial community. In order to achieve this, quantitative and metagenomic techniques were combined to characterize the microbiome of A. vulgare on multiple levels: (i) Field vs. lab populations, (ii) in different host tissues, and (iii) in relation to Wolbachia infection status, i.e. presence/absence of Wolbachia as well as infection with different Wolbachia strains. Wolbachia represented the predominant member of the bacterial community in infected individuals and was identified as an important factor influencing bacterial community structure. Apart from Wolbachia, we detected a second highly abundant bacterium: Candidatus Hepatoplasma crinochetorum, a facultative symbiont previously reported from the midgut caeca, was for the first time observed in all tested host tissues. The potential interactions of Wolbachia and Ca. H. crinochetorum constitute an interesting example for symbiont-symbiont relationships between two highly abundant members of a diverse bacterial community.