Probiotics are an alternative to increase broiler productivity and flock health. For this reason, the objective of the first study was to evaluate commercially available Bacillus spp. based probiotic products on their ability to reduce Salmonella Heidelberg, in vitro. Results showed that most products reduced the lower concentrations of S. Heidelberg and maintained a reduction for up to 8 h. The second study was conducted to determine if bacterial colonization occurred in a broiler chick after in ovo injection. Using bioluminescence, it was demonstrated that bacteria could migrate and colonize the embryo within 2 h after in ovo injection into the amniotic fluid. The results of these studies demonstrated that probiotics could reduce pathogenic microorganisms and can potentially have a positive impact on the chick before it even hatches and is placed in a broiler house.

Streptococcus pneumoniae (the pneumococcus) is one of the leading causes of death due to infectious disease in the world, with over one million deaths being attributed to this bacterium each year. While the majority of these deaths occur in children in developing nations, significant morbidity and mortality in the developed world, especially in the elderly, can be attributed to pneumococcal diseases such as bacterial pneumonia and meningitis. This is despite the near-universal use of anti-pneumococcal vaccines in these parts of the world. The work presented in this thesis describes the ways in which resident nasal macrophages respond to nasopharyngeal pneumococcal colonization, allowing for the protection of immunocompetent individuals from these diseases. This thesis describes the role of the macrophage scavenger receptor MARCO in recognizing the bacterium upon colonization, and the chain of events that are subsequently established. I have found that MARCO is vital in orchestrating the clearance of pneumococci from the nasopharynx in an expedient manner, as well as preventing the swift spread of bacteria to other tissues of the body early on in colonization. I also outline a role for regulatory micro-RNAs present in macrophages in the mounting of this anti-pneumococcal response via the induction of specific T cell populations. The collection of data found herein is an important resource for those attempting to understand the complex narrative that takes place between the pneumococcus and the innate immune system during a colonizing event and will lead to further discovery on how healthy individuals escape fatal pneumococcal disease. / Thesis / Doctor of Philosophy (PhD) / The bacterium Streptococcus pneumoniae is one of the most dangerous pathogens in the world, accounting for more one million deaths every year worldwide. This bacterium is also very common, with approximately one third of all people having some S. pneumoniae in their noses at any given time. The goal of this thesis is to provide a better understanding of how our immune cells interact with S. pneumoniae when it first enters our noses and how these initial interactions prevent healthy people from becoming sick. I have found that white blood cells called macrophages are crucial to these interactions. Macrophages are able to ‘eat’ the bacteria using a specialized protein called MARCO to grab onto them. This information will be vital in trying to develop new vaccines and treatments for S. pneumoniae-related diseases like bacterial pneumonia (lung infection) and meningitis (brain infection).

Animal hosts provide associated microorganisms with suitable ecological niches in their intestines. Microbes help their hosts to digest food, protect against pathogens, and influence the host’s metabolisms. Compositional variation of gut microbial communities is common among hosts, and may affect the health status of hosts. Diet and genetic factors are well known to influence the assembly of gut microbial communities. This thesis focuses on disentangling the contributions of factors including host genetics (sex), diet, environment, and other ecological processes to the assembly of gut microbial communities in freshwater fish. The association between gut microbial communities and fish condition is also evaluated in this thesis. Applying metacommunity theory, we found environmental factors including fish habitat, fish species, their diet, dispersal factors including microbes from fish diet, and ecological drift contributed to the assembly of fish gut microbial communities. The proportion of their contribution varied between fish species, where ecological drift explained more in perch than in roach. Under natural conditions fish populations face the risk of predation, which can induce competition and impose predation stress within prey individuals. This can therefore lead to changes in their diet qualities and quantities. In this thesis, it was shown that fish diet in terms of qualities and quantities significantly influenced the overall gut microbial composition, and this influence was dependent on fish sex, a host genetic factor. Predation stress was also suggested to significantly decrease the species richness. Furthermore, when fish were experiencing a diet shift, we showed that different bacterial phyla from novel food had different colonization success in the intestine, and this colonization success was positively influenced by predation stress. Fish condition was suggested in this thesis to be affected by gut microbial composition, especially by the contributions of the bacterial phyla Tenericutes and Actinobacteria.

O objetivo geral deste trabalho foi avaliar a influência do uso precoce de antimicrobianos na microbiota intestinal, resposta imune e ocorrência de diarreias em bezerras recém-nascidas. Foram selecionadas 26 bezerras Holandesas distribuídas de acordo com a aplicação (ATB+) ou não (ATB-) de tulatromicina (2,5 mg/Kg - SC) até 12h de vida. Capítulo 1 Este capítulo avaliou a influência do uso precoce de antimicrobiano na sanidade de bezerras holandesas recém-nascidas, por meio do exame clínico geral. As diarreias foram detectadas por sistema de escore e matéria seca (%) nas fezes, além do escore respiratório e palpação externa da região umbilical. O desempenho das bezerras foi determinado pela estimativa do ganho de peso. As bezerras ATB- apresentaram maior frequência de mucosas esbranquiçadas (P=0,066) e inflamações umbilicais no ATB- em D3-5 (P=0,063) e D13-15 (P= 0,066). A frequência de escore fecal 2 e 3 foi semelhante entre os grupos, observando-se pico no D13-15. Os valores médios para matéria seca (%) foram menores no ATB+ no D7-9 (P=0,063) e D27-30 (P=0,084). O agente etiológico das diarreias foi o Cryptosporidium e/ou rotavírus. O ganho de peso diário (GPD) foi igual entre grupos, observando-se intensa redução no GPD em D13-15. Capítulo 2 O objetivo deste capítulo foi avaliar a influência do uso precoce de antimicrobianos na colonização bacteriana intestinal, por meio da detecção de material genético dos principais grupos bacterianos por meio do PCR em tempo real. Não foram observadas diferenças entre os grupos para bactérias totais e C. perfringens. As bezerras ATB- apresentaram maior quantidade de Bifidobacterium, nas fezes no D3-5 (P=0,002) e D7-9 (P=0,018). A população de Lactobacillus também apresentou tendência (P=0,097) para maior número de cópias de DNA no grupo ATB-. Ao contrário, a Escherichia coli apresentou tendência para maiores valores no grupo ATB+ no D20-23 (P=0,052) e D27-30 (P=0,072). Capítulo 3 O objetivo deste capítulo foi avaliar a influência do uso precoce de antimicrobianos no perfil inflamatório de bezerras holandesas recém-nascidas por meio de provas hematológicas, imunológicas, bioquímicas e eletroforéticas. Observou-se tendência para menores valores de hemoglobina (P=0,071), CHCM (P=0,057) e ferro sérico (P=0,051) no D3-5 no ATB-. Neste momento, a frequência de anemias também foi maior no ATB- (P=0,016). O número de neutrófilos (P=0,051) e a produção espontânea de EROs foi maior no ATB-, enquanto o número de linfócitos foi maior no ATB+ (P=0,061) no D7-9. Estes dados são condizentes com as análises imunes, no qual a proporção de populações de mononucleares 1 e 2 expressando o CD62L+ apresentou tendência para maior valor no ATB+ em D3-5 (P=0,098) e D7-9 (P=0,083). Após as diarreias (D13-15), os granulócitos (P=0,043) e mononucleares (P=0,089) das bezerras ATB+ apresentaram maior intensidade de fluorescência para expressão CD62L no D20-23. O grupo ATB+ também apresentou maiores teores de beta-globulina (P=0,057), gama-globulina (P=0,069) e haptoglobina (P=0,032) no D13-15. O uso precoce de tulatromicina influenciou na microbiota intestinal, imunidade inata e ocorrência de doenças no período neonatal. / The general goal of this research was to evaluate the influence of early antimicrobial use in the gut microbiota, immune response and occurrence of diarrhea in neonate heifers. It was screened 26 neonate Holstein heifers distributed according to the application (ATB+) or not (ATB-) of tulathromycin (2.5mg/Kg - SC) from birth until 12 hours of life. Chapter 1 This chapter evaluated the influence of early use of antimicrobial in the health of neonate Holstein heifer by general clinical examination. Diarrheas were detected using score system and fecal dry matter (%), besides of respiratory score and external palpation of navel region. The performance of calves was evaluated by daily weight gain. Heifers ATB- had high frequency of paleness mucous (P=0.066) and umbilical inflammation in ATB- group on D3-5 (P=0.063) and D13-15 (P= 0.066). The frequency of fecal score 2 and 3 was similar between groups, observing peak of diarrhea on D13-15. The mean values of fecal dry matter were low in ATB+ group on D7-9 (P=0.063) and D27-30 (P=0.084). The main etiologic agent of diarrheas was Cryptosporidium and/or rotavírus. The daily weight gain (DWG) was similar between groups, observing intense decrease of DWG on D13-15. Chapter 2 The aim of this chapter was to evaluate the influence of early use of antimicrobial in the microbial gut colonization by detection of genetic bacterial material using real time PCR. It was not found difference between groups for total bacteria and C. perfringens. The calves from ATB- group had high quantity of Bifidobacterium in the fecal material on D3-5 (P=0.002) and D7-9 (P=0.018). The Lactobacillus population had a tendency (P=0.097) to have high number of DNA copies in the ATB- group. On the other hand, Escherichia coli had tendency to high values in ATB+ group on D20-23 (P=0.052) and D27-30 (P=0.072). Chapter 3 The aim of this chapter was to evaluate the influence of early use of antimicrobial in the inflammatory profile of neonate Holstein heifers by hematological, immunological and biochemical tests, besides electrophoresis. It was possible to observe lower values of hemoglobin (P=0.071), CHCM (P=0.057) and serum iron (P=0.051) in ATB- group on D3-5. In this moment, the frequency of anemia also was high in ATB- group (P=0.016). The number of neutrophils (P=0.051) and spontaneous ROSs was high in ATB- group, while the number of lymphocytes was high in ATB+ group (P=0.061) on D7-9. These data were according to immune analysis, where the proportion of mononuclear population 1 and 2 expressing CD62L+ had a tendency for high values in ATB+ group on D3-5 (P=0.098) and D7-9 (P=0.083). After diarrhea (D13-15), granulocytes (P=0.043) and mononuclear cells (P=0.089) showed high fluorescence intensity of CD62L in ATB+ heifers on D20-23. ATB+ group also had high rate of beta globulin (P=0.057), gamma globulin (P=0.069) and haptoglobin (P=0.032) on D13-15. The early use of tulathromycin had influence on gut microbiota, innate immunity and occurrence of disease in the neonatal period.

O objetivo geral deste trabalho foi avaliar a influência do uso precoce de antimicrobianos na microbiota intestinal, resposta imune e ocorrência de diarreias em bezerras recém-nascidas. Foram selecionadas 26 bezerras Holandesas distribuídas de acordo com a aplicação (ATB+) ou não (ATB-) de tulatromicina (2,5 mg/Kg - SC) até 12h de vida. Capítulo 1 Este capítulo avaliou a influência do uso precoce de antimicrobiano na sanidade de bezerras holandesas recém-nascidas, por meio do exame clínico geral. As diarreias foram detectadas por sistema de escore e matéria seca (%) nas fezes, além do escore respiratório e palpação externa da região umbilical. O desempenho das bezerras foi determinado pela estimativa do ganho de peso. As bezerras ATB- apresentaram maior frequência de mucosas esbranquiçadas (P=0,066) e inflamações umbilicais no ATB- em D3-5 (P=0,063) e D13-15 (P= 0,066). A frequência de escore fecal 2 e 3 foi semelhante entre os grupos, observando-se pico no D13-15. Os valores médios para matéria seca (%) foram menores no ATB+ no D7-9 (P=0,063) e D27-30 (P=0,084). O agente etiológico das diarreias foi o Cryptosporidium e/ou rotavírus. O ganho de peso diário (GPD) foi igual entre grupos, observando-se intensa redução no GPD em D13-15. Capítulo 2 O objetivo deste capítulo foi avaliar a influência do uso precoce de antimicrobianos na colonização bacteriana intestinal, por meio da detecção de material genético dos principais grupos bacterianos por meio do PCR em tempo real. Não foram observadas diferenças entre os grupos para bactérias totais e C. perfringens. As bezerras ATB- apresentaram maior quantidade de Bifidobacterium, nas fezes no D3-5 (P=0,002) e D7-9 (P=0,018). A população de Lactobacillus também apresentou tendência (P=0,097) para maior número de cópias de DNA no grupo ATB-. Ao contrário, a Escherichia coli apresentou tendência para maiores valores no grupo ATB+ no D20-23 (P=0,052) e D27-30 (P=0,072). Capítulo 3 O objetivo deste capítulo foi avaliar a influência do uso precoce de antimicrobianos no perfil inflamatório de bezerras holandesas recém-nascidas por meio de provas hematológicas, imunológicas, bioquímicas e eletroforéticas. Observou-se tendência para menores valores de hemoglobina (P=0,071), CHCM (P=0,057) e ferro sérico (P=0,051) no D3-5 no ATB-. Neste momento, a frequência de anemias também foi maior no ATB- (P=0,016). O número de neutrófilos (P=0,051) e a produção espontânea de EROs foi maior no ATB-, enquanto o número de linfócitos foi maior no ATB+ (P=0,061) no D7-9. Estes dados são condizentes com as análises imunes, no qual a proporção de populações de mononucleares 1 e 2 expressando o CD62L+ apresentou tendência para maior valor no ATB+ em D3-5 (P=0,098) e D7-9 (P=0,083). Após as diarreias (D13-15), os granulócitos (P=0,043) e mononucleares (P=0,089) das bezerras ATB+ apresentaram maior intensidade de fluorescência para expressão CD62L no D20-23. O grupo ATB+ também apresentou maiores teores de beta-globulina (P=0,057), gama-globulina (P=0,069) e haptoglobina (P=0,032) no D13-15. O uso precoce de tulatromicina influenciou na microbiota intestinal, imunidade inata e ocorrência de doenças no período neonatal. / The general goal of this research was to evaluate the influence of early antimicrobial use in the gut microbiota, immune response and occurrence of diarrhea in neonate heifers. It was screened 26 neonate Holstein heifers distributed according to the application (ATB+) or not (ATB-) of tulathromycin (2.5mg/Kg - SC) from birth until 12 hours of life. Chapter 1 This chapter evaluated the influence of early use of antimicrobial in the health of neonate Holstein heifer by general clinical examination. Diarrheas were detected using score system and fecal dry matter (%), besides of respiratory score and external palpation of navel region. The performance of calves was evaluated by daily weight gain. Heifers ATB- had high frequency of paleness mucous (P=0.066) and umbilical inflammation in ATB- group on D3-5 (P=0.063) and D13-15 (P= 0.066). The frequency of fecal score 2 and 3 was similar between groups, observing peak of diarrhea on D13-15. The mean values of fecal dry matter were low in ATB+ group on D7-9 (P=0.063) and D27-30 (P=0.084). The main etiologic agent of diarrheas was Cryptosporidium and/or rotavírus. The daily weight gain (DWG) was similar between groups, observing intense decrease of DWG on D13-15. Chapter 2 The aim of this chapter was to evaluate the influence of early use of antimicrobial in the microbial gut colonization by detection of genetic bacterial material using real time PCR. It was not found difference between groups for total bacteria and C. perfringens. The calves from ATB- group had high quantity of Bifidobacterium in the fecal material on D3-5 (P=0.002) and D7-9 (P=0.018). The Lactobacillus population had a tendency (P=0.097) to have high number of DNA copies in the ATB- group. On the other hand, Escherichia coli had tendency to high values in ATB+ group on D20-23 (P=0.052) and D27-30 (P=0.072). Chapter 3 The aim of this chapter was to evaluate the influence of early use of antimicrobial in the inflammatory profile of neonate Holstein heifers by hematological, immunological and biochemical tests, besides electrophoresis. It was possible to observe lower values of hemoglobin (P=0.071), CHCM (P=0.057) and serum iron (P=0.051) in ATB- group on D3-5. In this moment, the frequency of anemia also was high in ATB- group (P=0.016). The number of neutrophils (P=0.051) and spontaneous ROSs was high in ATB- group, while the number of lymphocytes was high in ATB+ group (P=0.061) on D7-9. These data were according to immune analysis, where the proportion of mononuclear population 1 and 2 expressing CD62L+ had a tendency for high values in ATB+ group on D3-5 (P=0.098) and D7-9 (P=0.083). After diarrhea (D13-15), granulocytes (P=0.043) and mononuclear cells (P=0.089) showed high fluorescence intensity of CD62L in ATB+ heifers on D20-23. ATB+ group also had high rate of beta globulin (P=0.057), gamma globulin (P=0.069) and haptoglobin (P=0.032) on D13-15. The early use of tulathromycin had influence on gut microbiota, innate immunity and occurrence of disease in the neonatal period.

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