O objetivo deste estudo foi avaliar o efeito da mistura comercial do líquido da casca de castanha de caju e do óleo de mamona (Essential, Oligo Basics Agroind. Ltda., Cascavel, Brasil) no desempenho, na microbiota e no sistema imune de frangos de corte desafiados ou não por coccidiose. Ao total 864 pintos machos (Cobb) de um dia de idade foram distribuídos aleatoriamente em 6 tratamentos (8 boxes/tratamento e 18 pintos/box) em um desenho fatorial 3 x 2 com 3 aditivos: controle (sem aditivo), 100 ppm de monensina ou 0,15% de Essential e 2 níveis de desafio aos 14 dias de idade: não desafiados ou inoculados por gavagem com 1mL de solução contendo oocistos esporulados de E. tenella, E. acervulina e E. máxima. Os resultados foram divididos em dois artigos. Artigo 1: Na primeira semana após desafio, as aves desafiadas suplementadas com monensina apresentaram maior ganho de peso (GP), consumo de ração (CR) e melhor conversão alimentar (CA) (P <0,05), porém na segunda semana o Essential apresentou maior GP e melhor CA (P <0,05), aos 42 dias de idade, ambos os grupos não se diferiram em GP, CR, PV e foram maiores do que o controle (P <0,05). A utilização de monensina em aves desafiadas reduziu o número cópias do domínio bactéria e de E.coli (P<0,05), por sua vez, a suplementação com Essential reduziu Clostridium Cluster XIV, Clostridium perfringens e Staphylococcus aureus em relação aos demais tratamentos (P<0,05). As aves não desafiadas que receberam Essential ou monensina apresentaram menor população de C.perfringens e S. aureus (P<0,05). Artigo 2: O grupo que recebeu Essential aumentou a expressão gênica de IFN-y, IL-6 e TNF-α (P<0,05) e o grupo controle aumentou a expressão gênica de COX-2 e IL-1 em relação aos demais tratamentos (P<0,05). As aves não desafiadas que receberam monensina apresentaram maior expressão gênica de IFN-y, COX-2 e IL-1 comparadas aos demais tratamentos (P<0,05), ao contrário do grupo com Essential que reduziu a expressão gênica com exceção do TNF-α. Aos 7 e 14 dias após o desafio houve maior excreção de oocistos para o grupo controle, Essential e monensina não diferiram-se (P>0,05). Assim, o Essential melhorou o desempenho de frangos de corte infectados por coccidiose após a segunda semana do desafio e atuou como um modulador da microbiota intestinal e do sistema imune, direcionando a resposta inflamatória contra o parasita. / The objective of this study was to evaluate the effects of a commercial mixture of cashew shell liquid and castor oil (Essential, Oligo Basics Agroind. Ltda., Cascavel, Brazil) on growth performance, immunity and microbiota in broilers challenged with coccidiosis. A total of 864 one-day-old male chicks (Cobb) were randomly assigned to 6 treatments (8 pens/treatment and 18 birds/pen) in a 3 x 2 factorial design with 3 additives: control (no additive), 100 ppm of monensin, and 0.15% of Essential; and 2 challenge levels at 14 days of age: no challenge and inoculation by gavage of 1 ml of a solution containing sporulated oocysts of E. tenella, E. acervulina, and E. maxima. The results were divided into two articles. Article 1: In the first week after challenge, challenged birds supplemented with monensin showed higher LW, WG, FI and better FCR (P <0.05), but in the second week Essential presented higher WG and better FCR (P <0.05), at 42 days of age, both groups did not differ in WG, FI, and LW and were higher than the control (P <0.05). The use of monensin in challenged birds reduced the number of copies of the bacteria domain and of E.coli (P<0,05). In turn, Essential supplementation reduced Clostridium Cluster XIV, Clostridium perfringens and Staphylococcus aureus in relation to the other treatments (P<0,05). The unchallenged birds that received Essential or monensin presented a lower population of C.perfringens and S. aureus (P<0,05). In addition, Essential presented higher number of copies of Lactobacillus spp., followed by monensin and control (P <0.05). Article 2: The group that received Essential increased the gene expression of IFN-y, IL-6 e TNF-α (P<0,05) and the control group increased the gene expression of COX-2 and IL-1 in relation to the other treatments (P <0.05). The unchallenged birds that received monensin presented upregulated expression of IFN-y, COX-2 and IL-1 compared to the other treatments (P <0.05), unlike the Essential group, which reduced gene expression with the exception of TNF-α. At 7 and 14 days after the challenge there was a higher excretion of oocysts for the control group, Essential and monensin did not differ (P>0,05). Thus, Essential improved the performance of coccidiosis-infected broiler chickens after the second week of challenge, as well as acts as a modulator of intestinal flora and immune system, directing the inflammatory response against the parasite.

O presente estudo busca fornecer subsídios para a evolução da qualidade de seleção da fiscalização da Compensação Financeira da Exploração Mineral (CFEM) visando a propiciar um aumento na recuperação de créditos em cada fiscalização. Pretende-se mensurar os parâmetros que possam ser utilizados na definição da priorização de empresas a serem auditadas in loco, com a construção, através de pesquisa exploratória por meio de análise documental e entrevistas com especialistas do setor da matriz de priorização. Com esta pesquisa, espera-se contribuir na otimização da arrecadação das receitas públicas, assim como melhorar os resultados através do aumento da eficácia das fiscalizações, ou seja, aumentando o grau de acerto das fiscalizações e reduzindo o número de fiscalizações sem resultado. A Auditoria Fiscal realizada pelo DNPM em empresas de mineração pode ser dividida nas seguintes etapas: Seleção da empresa; Observação dos Processos Operacionais da Empresa; Inspeção da Documentação Contábil, Fiscal e Gerencial; Relatório de Fiscalização; Lavratura da Notificação Fiscal de Lançamento de Débitos para Pagamento (NFLPD). Nesta pesquisa, foram utilizados métodos primários (entrevistas com especialistas do setor) e secundários de pesquisa como a revisão da literatura. O método Delphi foi utilizado para coletar a opinião dos especialistas do setor. Quanto à técnica, utilizou-se a matriz GUT (Gravidade, Urgência, Tendência) que tem como objetivo estabelecer as prioridades das ações entre diversas alternativas, em que são atribuídos graus de importância nos valores de 1 a 5 para cada um dos problemas que compõe essa matriz. Na fase de entrevistas, identificou-se o nível de consenso e a prioridade dos critérios para seleção de empresas para fins de auditoria da CFEM. Concluiu-se que a adoção de critérios para direcionamento das auditorias externas da CFEM é mais eficiente do que a seleção aleatória realizada atualmente na SUP/DNPM/RS. Propõe-se que essa conclusão seja considerada em futuros planejamentos na SUP/DNPM/RS, para produzir melhorias em termos de arrecadação da CFEM e para tornar o processo de seleção eficiente. / The present study seeks to provide subsidies for the evolution of the selection quality of the Financial Compensation for Mineral Exploration (FCME) supervision in order to provide an increase in the recovery of credits in each inspection. It is intended to measure the parameters that can be used to define the prioritization of companies to be audited in loco, with the construction, through exploratory research through documentary analysis and interviews with specialists of the sector of the prioritization matrix. With this research, we hope to contribute to the optimization of the collection of public revenues, as well as to improve the results by increasing the efficiency of the inspections, that is, increasing the degree of correctness of the inspections and reducing the number of inspections without result. The Fiscal Audit carried out by DNPM in mining companies can be divided into the following stages: Company selection; Observation of the Company's Operating Processes; Inspection of Accounting, Tax and Management Documentation; Inspection Report; Drawing up of the Tax Notification of Debits for Payment (TNDP). In this research, primary (interviews with industry experts) and secondary research methods were used as the literature review. The Delphi method was used to gather the opinion of industry experts. As for the technique, the GUT (Severity, Urgency, Tendency) matrix was used to establish the priorities of the actions among several alternatives, in which degrees of importance are assigned in the values from 1 to 5 for each of the problems that compose this matrix. In the interview phase, the level of consensus and the priority of the criteria for company selection for FCME audit purposes were identified. It was concluded that the adoption of criteria to guide FCME's external audits is more efficient than the current random selection performed at SUP/DNPM/RS. It is proposed that this conclusion be considered in future SUP/DNPM/RS planning to produce improvements in terms of FCME collection and to make the selection process efficient.

The main objective of the diploma thesis was defined as the consideration of the hypothesis that food intake structure of adult roach changes significantly during the spawning period. The practical experiment was conducted to reach the defined aim. The experiment was performed on the Brno and Hamry Reservoirs in 2008 and 2009. The acquired data were analysed by standard tools used for gut contents analyses (Indirect Method, Frequency of Occurrence, Index of Fullness, Index of Preponderance) related to the Gonadosomatic Index.

Introdução: o estresse psicológico aumenta a permeabilidade intestinal em roedores e humanos, potencialmente levando a inflamação de baixo grau e aos sintomas em distúrbios gastrintestinais funcionais. No entanto, o efeito do estresse agudo combinado ao estresse da vida crônica, que mimetiza potencialmente melhor a situação humana, é desconhecido. Além disso, há poucos dados disponíveis sobre os efeitos do estresse em intestino delgado versus cólon. Métodos: ratos Wistar foram alocados em quatro protocolos de estresse: 1/ controles; 2/ estresse agudo (isolamento e movimentos limitados); 3/ Crowding stress:crônico e 4/ estresse agudo + estresse crônico. Amostras de jejuno e cólon foram colhidas para estudar a permeabilidade em câmaras deUssing, a expressão gênica de moléculas de junção firmes e a densidade de mastócitos. Níveis de corticosterona no plasma foram medidos. Principais resultados:corticosterona plasmática foi avaliada nas três condições de estresse, teve níveis mais altos na condição de estresse combinado. Permeabilidade do jejuno foi aumentada em todas as condições de estresse e correlacionada com os níveis de corticosterona. O aumento da expressão das claudinas 1, 5 e 8, daocludina e da ZO-1 foi detectado no estado de estresse agudo no jejuno. Em contraste, a permeabilidade do cólon foi aumentada no protocolo de estresse combinado, e a expressão de moléculas das junção firmes permaneceu inalterada. O aumento da densidade de mastócitos foi observado no cólon nos ratos submetidos aos estresses crônico e combinado. Conclusão e inferências:os estresses agudo, crônico e combinado influenciam diferentemente a permeabilidade intestinal, a expressão de moléculas de junção firmes e a atividade dos mastócitos, no jejuno e no cólon. Estes resultados fornecem uma visão mais aprofundada dos mecanismos de hiperpermeabilidade intestinal relacionadas ao estresse. / Background: Psychological stress increases intestinal permeability in rodents and humans, potentially leading to low-grade inflammation and symptoms in functional gastrointestinal disorders through disturbances in brain-gut axis. However, the effect of acute stress on the background of Crhonic life stress, potentially better approaching the human situation, is unknown. Moreover, only limited information is available on the effects in small intestine versus colon in animal model. Methods: Wistar rats were allocated to 4 stress protocols: 1/ sham; 2/ acute stress (isolation and limited movement); 3/ Crhonic crowding stress and 4/ acute + Crhonic stress (n = 8 per group). Jejunum and colon were harvested to study permeability in Ussing chambers, gene expression of tight junction molecules and mast cell density. Plasma corticosterone levels were measured. Key Results: Plasma corticosterone was elevated in all three stress conditions, with the highest levels in the combined stress condition. Permeability of the jejunum was increased in all stress conditions and correlated with corticosterone levels. Increased expression of claudin 1, 5 and 8, occludin and ZO-1 was detected in the acute stress condition in the jejunum. In contrast, colonic permeability was increased in the acute on Crhonic stress protocol only and the expression of tight junction molecules was unaltered. Increased mast cell density was observed in the Crhonic and acute on Crhonic stress condition in the colon only. Conclusion and Inferences: Acute, Crhonic and combined stress differentially affect intestinal permeability, expression of tight junction molecules and mast cells in the jejunum and the colon. These findings provide further insight in the mechanisms of stress-related intestinal hyperpermeability and barrier.

O objetivo deste trabalho foi avaliar a adição de diferentes níveis de levedura (Saccharomyces cerevisiae) inativa e desidratada às rações, associados ao plasma sangüíneo e ao ácido glutâmico, sobre o desempenho e morfologia intestinal de leitões na fase inicial. Para tanto, foram realizados dois experimentos, cada um com três tratamentos de quatro repetição com 22 animais em fase de creche (21 à 59 dias), totalizando 264 leitões por experimento. Os animais foram distribuídos em delineamento em blocos casualizados nos dois experimentos. Ambos foram divididos em quatro fases experimentais correspondentes as trocas das dietas: pré - inicial 1(21-28), pré - inicial 2 (29-35), pré - inicial 3 (36-42). O experimento 1 teve os seguintes tratamentos: Ração Pré Inicial 1 - A - 5% de levedura inativa, 4% de plasma, 1% de ácido glutâmico; B - 3% de levedura inativa, 2% de levedura hidrolisada, 4% de plasma e 1% de ácido glutâmico; C - 3% de levedura inativa, 2% de levedura hidrolisada, 4% de plasma. Ração Pré Inicial 2 - A - 4% de levedura inativa, 3% de plasma, 0,8% de ácido glutâmico; B - 3% de levedura inativa, 1% de levedura hidrolisada, 3% de plasma e 0,8% de ácido glutâmico; C - 3% de levedura inativa, 1% de levedura hidrolisada, 3% de plasma. Ração Pré Inicial 3 - A - 2% de levedura inativa, 1,5% de plasma, 0,6% de ácido glutâmico; B - 2% de levedura, 0,5% de levedura hidrolisada, 1,5% de plasma e 0,6% de ácido glutâmico; C - 2% de levedura, 0,5% de levedura hidrolisada, 1,5% de plasma. E o experimento 2 teve os seguintes tratamentos: Ração Pré Inicial 1 - A - 5% de levedura inativa, 3% de plasma; B - 5% de levedura inativa, 3% de plasma e 1% de ácido glutâmico; C - 3% de levedura inativa, 2% de levedura hidrolisada, 3% de plasma e 1% de ácido glutâmico. Ração Pré Inicial 2 - A - 4% de levedura inativa, 2% de plasma; B - 4% de levedura inativa, 2% de plasma, 0,8% de ácido glutâmico; C - 3% de levedura inativa, 1% de levedura hidrolisada, 2% de plasma e 0,8% de ácido glutâmico. Ração Pré Inicial 3 - A - 2% de levedura inativa, 1,0% de plasma; B - 2% de levedura inativa, 1,0% de plasma, 0,6% de ácido glutâmico; C - 2% de levedura, 0,5% de levedura hidrolisada, 1,0% de plasma e 0,6% de ácido glutâmico. A levedura hidrolisada demonstrou aspectos positivos para sua utilização em dieta de leiões nas fases críticas pós desmama podendo promover melhora no desempenho zootécnico e na morfologia intestinal dos animais. / The objective of this study was to evaluate the addition of different levels of hidrolysed and inactive yeast (Saccharomyces cerevisiae) in feed, with spray dried blood plasma and glutamic acid on performance and intestinal morphology of weaned piglets. Two experiments were conducted, each with three treatmens, four replicates with 22 animals in the nursery phase (21 to 59 days of age), totaling 264 pigs per experiment. The piglets were distributed in randomized block design in both experiments. The experiments were divided in four phases corresponding experimental diets: pre - starter 1 (21-28), pre - starter 2 (29-35), pre - starter 3 (36-42). Experiment 1 had the following treatments: Pre starter 1 - A - 5% of inactive yeast, 4% plasma, 1% glutamic acid; B - 3% of inactive yeast, 2% hydrolyzed yeast, 4% plasma and 1% glutamic acid; C - 3% inactive yeast, 2% hydrolyzed yeast, 4% of plasma. Pre starter 2 - A - 4% inactive yeast, 3% plasma, 0.8% glutamic acid; B - 3 % inactive yeast, 1% hydrolyzate yeast, 3% plasma, 0.8% glutamic acid; C - 3% inactive yeast, 1% hydrolyzate yeast, 3% of plasma. Pre starter 3 - 2% inactive yeast, 1.5% plasma, 0.6% glutamic acid; B - 2% inactive yeast, 0.5% hydrolyzate yeast, 1.5% and plasma 0 6% glutamic acid; C - 2% inactive yeast, 0.5% hydrolyzate yeast, 1.5% plasma. And the experiment 2 had the following treatments: Pre starter 1 - A - 5% inactive yeast, 3% plasma; B - 5% inactive yeast, 3% plasma and 1% glutamic acid; C - 3% inactive yeast , 2% hydrolyzate yeast, 3% plasma and 1% glutamic acid. Pre starter 2 - A - 4% inactive yeast, 2% plasma; B - 4% inactive yeast, 2% plasma, 0.8% glutamic acid; C - 3% inactive yeast, 1% hydrolyzate yeast, 2 % plasma and 0.8% of glutamic acid. Pre starter 3 - A - 2% inactive yeast, 1.0% plasma; B - 2% inactive yeast, 1.0% plasma, 0.6% glutamic acid; C - 2% inactive yeast, 0, 5% hydrolyzate yeast 1.0% of plasma and 0.6% glutamic acid. Yeast hydrolyzate showed positive aspects to their use in diet after weaning can promote improvement in performance and intestinal morphology of animals.

O desenvolvimento de biotecnologia de embriões em animais de produção é prejudicado por perdas no primeiro trimestre da gestação, idade em que o intestino primitivo está sendo estabelecido. O estudo das proteínas contidas no intestino primitivo nesta fase inicial da gestação pode aumentar o conhecimento sobre as vias moleculares envolvidas no desenvolvimento embrionário normal e em perdas de embriões, assim como a sua participação na organogênese e diferenciação celular. Intestino primitivo de embriões de bovinos a partir dos 39 SD ± 4 dias de desenvolvimento (variando de 33 a 45 dias) foram coletados em um matadouro local. As amostras foram processadas e agrupadas para análise proteômica shotgun label-free usando MudPIT (Multidimensional Protein Identification Technology). Análise funcional e de via foram feitas usando FatiGO (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) para identificar as ontologias relevantes e vias canônicas ou não-canônicas representada pelas proteínas expressas no Intestino primitivo. Um total de 74 proteínas ou sequências randômicas foram identificadas, correspondentes a 30 proteínas específicas expressas pelo Intestino primitivo bovino. Das 30 proteínas únicas, 21 proteínas foram utilizadas na ontologia e análise de vias. As análises mostraram um enriquecimento de ontologias relacionadas com a ligação (N = 5); atividade catalítica (N = 6); organela intracelular (N = 6). Houve um enriquecimento de ontologias associado às modificações do citoesqueleto; processo de diferenciação celular (N = 3), a migração celular (N = 4) e no metabolismo celular (N = 6). Além disso, a via e a análise de rede mostraram um enriquecimento de vias de comunicação entre células, tais como junções comunicantes e tight e as vias de adesão focal. Além disso, as vias envolvidas no movimento celular (por exemplo, vias de regulação do citoesqueleto de actina e a migração transendotelial de leucócitos) foram extremamente enriquecimento no grupo de proteínas expressas pelo Intestino primitivo bovino. Nossos resultados sugerem que as células do intestino primitivo tem alto perfil migratório e são compostas de células não totalmente diferenciadas, com alto metabolismo celular. A migração e a diferenciação destas células poderiam determinar o destino do embrião em desenvolvimento. Além disso, a compreensão da função e interação de proteínas expressas pelo embrião normal fornecerá informações sobre o impacto das biotecnologias reprodutivas no desenvolvimento do embrião durante a implantação e placentação. / The development of embryo biotechnology in farm animals is hampered by embryo losses in first trimester of gestation, period in which the primitive gut is being established. The study of proteins contained in the primitive gut at this early stage of pregnancy may increase the knowledge about the molecular pathways involved in normal embryonic development and loss of embryos, as well as their involvement in organogenesis and cell differentiation.primitive gut from bovine embryos on day 39 SD± 4 of development (ranging from 33 to 45 days) were collected at a local slaugtherhouse. The samples were processed and pooled for label-free shotgun proteomics analysis using MudPIT (Multidimensional Protein Identification Technology) tandem MSE acquisition. Functional and pathway analysis using FatiGo (www.babelomics.org); Pathway Express (http://vortex.cs.wayne.edu/ ontoexpress) and Ingenuity Pathway Analysis (www.ingenuity.com) were used to identify relevant ontologies and canonical or noncanonical pathways represented by the expressed proteins in the primitive gut. A total of 74 protein sequences were identified corresponding to 30 unique proteins expressed by the bovine primitive gut. out of 30 unique proteins, 21 proteins were used on the ontology and pathway analysis. The ontology analysis showed an enrichment of ontologies related to binding (N=5); catalytic activity (N=6); intracellular organelle (N=6). There was an enrichment of ontologies associated to cytoskeleton modifications; cell differentiation process (N=3); cellular migration (N=4) and cell metabolism (N=6). Furthermore, the pathway and the network analysis showed an enrichment of cell-to-cell communication pathways such as gap and tight junction, and focal adhesion pathways. In addition, pathways involved in cellular movement (regulation of actin cytoskeleton and leukocyte transendothelial migration) were extremely enrichment in the group of proteins expressed by the bovine primitive gut. Our results suggested that the cells from primitive gut have high migratory profile and are composed of not fully differentiated cells with high cellular metabolism. The proper migration and differentiation of these cells would dictate the fate of the developing embryo. Moreover, understanding the function and interaction of proteins expressed by normal embryo will give clues of the impact of the reproductive biotechnologies in embryo development during the window between implantation and placentation.

The availability of high-throughput sequencing technologies has enabled metagenomicinvestigations into complex bacterial communities with unprecedented resolution andthroughput. The production of dedicated data sets for metagenomic analyses is, however, acostly process and, frequently, the first research questions focus on the study species itself. Ifthe source material is represented by fecal samples, target capture of host-specific sequencesis applied to enrich the complex DNA mixtures contained within a typical fecal DNA extract.Yet, even after this enrichment, the samples still contain a large amount of environmentalDNA that is usually left unanalysed. In my study I investigate the possibility of using shotgunsequencing data that has been subjected to target enrichment for mtDNA from the hostspecies, Grauer’s gorilla (Gorilla beringei graueri), for further analysis of the microbialcommunity present in these samples. The purpose of these analyses is to study the differencesin the bacterial communities present within a high-altitude Grauer’s gorilla, low-altitudeGrauer’s gorilla, and a sympatric chimpanzee population. Additionally, I explore the adaptivepotential of the gut microbiota within these great ape populations.I evaluated the impact that the enrichment process had on the microbial community by usingpre- and post-capture museum preserved samples. In addition to this, I also analysed the effectof two different extraction methods on the bacterial communities.My results show that the relative abundances of the bacterial taxa remain relatively unaffectedby the enrichment process and the extraction methods. The overall number of taxa is,however, reduced by each additional capture round and is not consistent between theextraction methods. This means that both the enrichment and extraction processes introducebiases that require the usage of abundance-based distance measures for biological inferences.Additionally, even if the data cannot be used to study the bacterial communities in anunbiased manner, it provides useful comparative insights for samples that were treated in thesame fashion.With this background, I used museum and fecal samples to perform cluster analysis to explorethe relationships between the gut microbiota of the three great ape populations. I found thatpopulations cluster by species first, and only then group according to habitat. I further foundthat a bacterial taxon that degrades plant matter is enriched in the gut microbiota of all threegreat ape species, where it could help with the digestion of vegetative foods. Another bacterialtaxon that consumes glucose is enriched in the gut microbiota of the low-altitude gorilla andchimpanzee populations, where it could help with the modulation of the host’s mucosalimmune system, and could point to the availability of fruit in the animals diet. In addition, Ifound a bacterial taxon that is linked with diarrhea in humans to be part of the gut microbiotaof the habituated high-altitude gorilla population, which could indicate that this pathogen hasbeen transmitted to the gorillas from their interaction with humans, or it could be indicative ofthe presence of a contaminated water source.

This body of research explores the dietary application of a bioactive, solid-state fermentation (SSF) product in contemporary and lupin-containing diets of Nile tilapia (Oreochromis niltoticus) and rainbow trout (Oncorhynchus mykiss). Consequently, the work provides holistic assessment of the influences of SSF products on animal health and performance; depending upon rearing temperature, nutritional physiologies, feed formulations and extrusion conditions; alongside information on the performance of lupins in aquafeeds. The SSF product (at 0.1 % inclusion) improved growth performance of Nile tilapia fed diets containing lupins. Phosphorous retention appeared higher when the SSF product was included in a yellow lupin (Lupinus luteus) diet whilst Mg retention was significantly higher in fish fed narrow-leaf lupin (Lupinus angustifolius). The experimental ingredients did not appear to show any clear effects upon midgut macrostructure. At an ultrastructural level, the fish fed yellow lupin alone, displayed poorest brush border characteristics but those fed yellow lupin and the SSF product showed signs of amelioration since they did not differ significantly from those fed narrow-leaf lupin. Focus was then turned towards a yellow lupin-based diet in rainbow trout, with two inclusion levels of the SSF product. The SSF product significantly improved growth performance and feed efficiency at 0.5 %, with values closer to a fishmeal-based diet than the lupin control. The SSF product increased the digestibility of protein and energy and bioavailability of numerous elements. However, the digestibility and bioavailability of certain nutrients, e.g. fibre and Zn, were only increased with a 0.5 % inclusion. The SSF product influenced vertebral Ca:P ratio but no effect on vertebral morphology was identified. Fish fed yellow lupin kernel meal displayed high Mn concentrations throughout a number of tissues. The intestinal environment was explored in depth, revealing large differences dependent upon SSF product inclusion rate. Fish fed a 0.1 % inclusion exhibited deteriorated brush border characteristics and high diversity of microbes, including increased proportions of key salmonid pathogens. Those fed a 0.5 % inclusion displayed signs of increased surface area at an ultrastructural level, reduced goblet cell numbers and a low microbial diversity; with domination of one particular family, Enterobacteriaceae. Activities of alkaline phosphatase and leucine aminopeptidase within the anterior intestine also appeared to be influenced by SSF product inclusion. Variations in haemato-immunological parameters were also observed between the treatments. In the final experiment, the SSF product was applied, pre-extrusion, to a contemporary rainbow trout formulation, at 0, 0.5, 1.0 and 1.5 %. No significant improvements to performance were identified following SSF product inclusion. However, crude protein digestibility from SSF-supplemented diets was significantly higher than the control and tendencies towards elevated retention of Ca, P, and Mg were apparent. In vitro analysis of free-phosphate release was conducted upon pre- and post-extruded diets, at varying temperatures. This indicated that neither extrusion conditions (105 °C) nor an ambient temperature of 10 °C were sufficient to cease P-liberating capabilities by the SSF product; suggesting that the two conditions combined limited the product’s efficacy in practice. This research evidenced that SSF products can be an effective means of improving the available nutrient profiles of compound diets for both omnivorous, warmwater and carnivorous, temperate finfish. Lupins are a promising alternative protein source but their nutritional value can be substantially improved by SSF product application. Exploration of the effects of SSF products on the intestinal environment revealed that both negative and positive effects on intestinal health can occur, which is highly dependent upon product inclusion rate. The holistic approaches adopted within this series of studies have seldom been performed on monogastric animals and thus provide valuable, transferable information for advancing knowledge in the application of SSF products, exogenous enzymes and lupins to farm animal feeds, in general.

Les pathologies intestinales sont des maladies multifactorielles dont l’incidence ne cesse d’augmenter. Les maladies organiques regroupent les maladies inflammatoires chroniques de l'intestin tel que la maladie de Crohn (MC) et les pathologies fonctionnelles digestives comprennent les différentes formes du syndrome de l'intestin irritable (SII). Ces pathologies présentes des caractéristiques communes comme des troubles du transit, des douleurs abdominales, un dysfonctionnement de la barrière intestinale et des modifications de la communication bidirectionnelle de l’axe intestin-cerveau et une altération de la composition du microbiote intestinal (dysbiose). Cette dernière peut être en partie associée à un déficit de production en peptides et protéines antimicrobiennes (PAMs) par les cellules de Paneth. Parmi les cibles thérapeutiques stratégiques, une réduction de la dysbiose dans le but de réduire l’état inflammatoire ou micro-inflammatoire de la muqueuse font aujourd’hui l’objet de différentes études. Ces traitements alternatifs montrent l’efficacité d’un régime nutritionnel adapté, d’un apport en probiotiques ou en prébiotiques sur le microbiote intestinal des patients MC et SII, et sur l’intégrité de leur barrière intestinale. Parmi les matrices alimentaires présentant une composition nutritionnelle intéressante proche du lait maternel humain, le lait d’ânesse (LA) contient également une forte teneur en PAMs (lysozyme). En parallèle, un observatoire économique et social de la filière asine commandité par l’Institut National Âne et Mulet fait le diagnostic d’une activité grandissante autour du LA chez les éleveurs français et montre, face à une concurrence italienne et chinoise importante, la nécessité d’une meilleure organisation de la filière via une meilleure valorisation du LA. L’objectif de cette thèse était d’évaluer un potentiel effet santé du LA et d’apporter des preuves scientifiques robustes pour permettre une meilleure valorisation de ce dernier. Ainsi, l’effet d’une consommation orale chronique de LA a été évalué sur deux modèles précliniques murins distincts : un modèle d’iléite expérimentale induite par une administration per os d’indométacine et un modèle de stress psychologique chronique (Water Avoidance Stress, WAS). Dans ce travail, le rôle clé de l’activité du lysozyme dans les effets observés a également été évalué. Des essais de traitements thermiques ont aussi été réalisés pour optimiser un barème de pasteurisation permettant de proposer un LA répondant aux normes réglementaires microbiologiques et sanitaires tout en conservant l’activité du lysozyme contenue dans le lait. Les travaux de cette thèse montrent que le LA possède des propriétés anti-inflammatoires se traduisant par une réduction significative des lésions inflammatoires macroscopiques et microscopiques de l’iléon. Cet effet est associé à une réduction de la dysbiose intestinale et normalise les niveaux de PAMs dans les cellules de Paneth drastiquement réduits lors de l’iléite. Dans le modèle WAS, le LA et la fraction contenant l’activité en lysozyme réduisent l’hypersensibilité viscérale, l’état micro-inflammatoire induites par le stress et restaurent les niveaux de PAMs dans les cellules de Paneth réduits par le stress. Un traitement thermique de 2 min/72°C permet d’augmenter la durée de vie du LA tout en conservant l’activité du lysozyme et ses propriétés santé sur la muqueuse intestinale chez la souris. / Gut pathologies are multifactorial with a constant increasing incidence. Organic diseases include inflammatory bowel diseases such as Crohn's disease (CD) and functional pathologies include various subtypes of irritable bowel syndrome (IBS). These pathologies present common features such as transit disorders, abdominal pain, dysfunction of the intestinal barrier associated with bidirectional gut-brain axis modifications and alterations of the gut microbiota composition (dysbiosis). Dysbiosis is generally associated with a lack of production of antimicrobial peptides and proteins (AMPs) by Paneth cells. Among the alternative treatment strategies, it has been proposed to reduce gut inflammation by correcting intestinal dysbiosis. Recent studies show the efficacy of a suitable diet, probiotics or prebiotics interventions on gut microbiota and on the integrity of their intestinal barrier in CD and IBS patients. Among interesting food matrices, donkey milk (DM) is a good candidate with a nutritional composition close to human breast milk and contains high levels of AMPs like lysozyme. An economic and social observatory of the donkey industry was ordered by the Institut National Âne et Mulet for a better support of growing French activity around DM against Italian and Chinese competitions. The objective of this thesis was to evaluate the potential beneficial healthy effect of DM and to provide robust scientific evidences for a better valorization of this product. Thus, the effect of chronic oral intake of DM was evaluated on two distinct murine preclinical models: a model of experimental ileitis induced by an oral administration of indomethacin and a model of chronic psychological stress (Water Avoidance Stress, WAS). In these studies, the key role of lysozyme activity in the observed effects was highlighted. In order to develop the DM market in France, thermal treatments have been carried out to optimize a pasteurization process to obtain a DM in accordance with the regulatory microbiological and sanitary standards while preserving the activity of the lysozyme contained in milk. The work of this thesis shows that DM exerts anti-inflammatory properties resulting in a significant reduction of the macroscopic and microscopic inflammatory lesions of the ileum. This effect is associated with a reduction of gut dysbiosis while normalizing the level of drastically reduced AMPs contained Paneth cells in the ileitis model. In the WAS model, DM and the fraction containing activity of lysozyme reduce visceral hypersensitivity, stress-induced gut microinflammatory status and also restore the level of AMPs in Paneth cells . A heat treatment at 2 min/72 °C allows to increase the shelf-life of DM while preserving the activity of lysozyme and its gut beneficial healthy properties in mouse.

La période des 1000 premiers jours de vie constitue une fenêtre de sensibilité au cours de laquelle l’environnement peut moduler le développement du foetus et du nourrisson, et conditionner la santé tout au long de la vie. Les conséquences à long terme de l’environnement périnatal sur le risque de maladies intestinales sont toutefois encore peu connues. L’objectif de ce travail était de montrer l’impact de l’environnement nutritionnel précoce sur la maturation intestinale et la santé intestinale à long terme.Un retard de croissance postnatal (RCPN) était induit chez la souris FVB/NRj par augmentation de la taille des portées. Le RCPN était responsable d’un retard de maturation de l’intestin chez la souris au sevrage, en particulier de la barrière intestinale, caractérisé par une augmentation de la perméabilité intestinale, concomitante d’une désorganisation des protéines des jonctions serrées. Le microbiote intestinal était moins riche en espèces bactériennes chez la souris au sevrage en cas de RCPN et sa composition était différente, avec en particulier une proportion anormalement élevée de Parabacteroides spp, Enterococcus spp, Erysipelatoclostridium spp, Eubacterium coprostanoligenes spp, Staphylococcus spp, et Escherichia-Shigella spp, et une plus faible proportion d’espèces productrices de butyrate. L’absence de barrière intestinale efficace et la dysbiose induites par le RCPN, étaient associées à une altération de la réponse inflammatoire de l’intestin à l’âge adulte, caractérisée par une augmentation des réponses immunitaires Th1, Th17 et Treg et une plus grande susceptibilité à la colite chimiquement induite.Ce travail démontre l’importance de l’environnement nutritionnel précoce dans la programmation de la santé intestinale au cours de la vie, et conforte l’hypothèse d’une origine développementale des maladies intestinales chroniques. / The first thousand days of life are a critical time for the development of both the fetus and the infant, and can modify the risk profile for diseases in later life. However, the longterm consequences of the perinatal environment on the susceptibility to intestinal disorders have not yet been assessed. The aim of the present study was to investigate the impact of the early nutritional environment on intestinal maturation and gut health in later life.Postnatal growth restriction (PNGR) was induced in FVB/NRj mice during the suckling period by adjusting the litter size. PNGR delayed intestinal maturation in pups at weaning. PNGR was associated with a maturation delay of the intestinal barrier, characterized by an increased intestinal permeability and impaired tight junctions. At the same time, PNGR affected gut bacterial colonization. Pups with PNGR harbored a decreased bacterial diversity, higher Parabacteroides spp, Enterococcus spp, Erysipelatoclostridium spp, Eubacterium coprostanoligenes spp, Staphylococcus spp, and Escherichia-Shigella spp, and lower butyrate producers. The lack of an efficient intestinal barrier and the dysbiosis induced by PNGR were associated with an altered intestinal inflammatory response in adult mice, characterized by an increase of Th1, Th17 and Treg immune responses, and a higher susceptibility to chemically induced colitis.Our data emphasize the importance of the early nutritional environment in programming of gut health in later life, and support the hypothesis of the developmental origin of chronic intestinal disorders.