Allergic diseases, for example asthma and eczema, are nowadays considered belonging to the most common chronic diseases amongst children in the West, but the cause for this increase in allergy prevalence is unknown. Since studies have indicated a connection between children's exposure of microorganisms during infancy and risk of developing allergic disease, it is suggested that this exposure is a crucial factor in question of allergy development or not. Other studies have established differences in microflora composition between healthy children and children with allergic disease, and several studies have shown that probiotic therapy can give positive results in both prevention and treatment of allergic diseases. The aim of this master's thesis was to develop a method, using PCR and denaturing gradient gel electrophoresis, to study the diversity of Lactobacillus spp. in fecal samples retrieved from a study of the probiotic strain L. reuteri ATCC 55730. The developed method was successful in detecting lactobacilli in fecal samples, but three other bacterial genera commonly found in humans were also amplified. Comparison of average numbers of detected bacterial strains and lactobacilli strains between samples belonging to the probiotics and placebo groups, respectively, showed higher numbers for the probiotics group. Also, the only fecal samples that contained L. reuteri belonged to the probiotics group. Although the results are far from statistically significant, they support the theories that probiotics may influence the intestinal microbiota.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第25357号 / 農博第2623号 / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 保川 清, 教授 井上 和生, 教授 谷 史人 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

A imunidade passiva surge como uma alternativa para a manipulação da fermentação ruminal e anticorpos de origem aviária contra bactérias específicas começam a ser pesquisados. Objetivou-se com este trabalho avaliar um preparado de anticorpos policlonais contra Streptococus bovis, Fusobacterium necrophorum e algumas cepas de bactérias proteolíticas (Peptostreptococcus anacrobius, Clostridium aminophilum e Clostridium sticklandii) sobre a diversidade microbiana ruminal e degradabilidade in situ de alguns alimentos. Foram utilizadas nove vacas mestiças portadoras de cânula ruminal. O delineamento experimental foi o quadrado latino 3 x 3 replicado 3 vezes, com arranjo fatorial de tratamentos 3 x 3 referente a 2 modificadores ruminais representados pela monensina (MON) e pelo preparado de anticorpos policlonais (PAP) mais o grupo controle e 3 fontes energéticas suplementadas na dieta, representadas pelo milho seco moído (MSM), silagem de grão úmido de milho (SGUM) e polpa cítrica (PC). Cada subperíodo experimental foi composto de 21 dias, sendo 16 dias para adaptação aos tratamentos e 5 para coleta de dados. A degradabilidade in situ dos alimentos testados foi mensurada através da técnica de saco de náilon. A coleta de amostras para a análise quantitativa de protozoários ocorreu no 21° dia de cada período, às 0 e 4 horas pós-alimentação, sendo estas coletadas por varredura do assoalho ruminal. O conteúdo ruminal foi coletado no 21° dia de cada período, às 4 h pós-alimentação, para análise da diversidade microbiana através de técnica de eletroforese em gel com gradiente de desnaturação. Observou-se que dietas contendo PC apresentaram aumento de 80,6%; 75,4% e 66,8% da degradabilidade efetiva da FDN da cana-de-açúcar para as taxas de passagem de 2, 5, 8%/h, respectivamente, em relação ao grupo tratado com SGUM, mas não em relação ao grupo com MSM. O tratamento com PAP demonstrou efeito sobre a fração solúvel (a) do amido do MSM, diminuindo esta em 45,26% e 45,37% em relação ao grupo CON e grupo MON, respectivamente. Observou-se que o tratamento com MON diminuiu em 16,14% o valor da fração potencialmente degradável (b) da MS da SGUM em relação ao grupo CON, mas não em relação ao grupo tratado com PAP. Já sobre a taxa de degradação (c), a MON aumentou o valor desta em 63,18% e 60,65% em relação ao grupo CON e PAP, respectivamente. Também a MON diminuiu a degradabilidade potencial (Dp) da MS da SGUM em 3,40% em relação ao grupo CON, mas não em relação ao grupo tratado com PAP. Observou-se que o PAP aumentou em 93,65% a contagem relativa de Isotricha em relação ao grupo CON, mas não em relação ao grupo MON. Já a PC aumentou em 334,42% (0h) e 399,75% (4h) a contagem relativa de protozoários do gênero Isotricha em relação às dietas de MSM e SGUM. Observou-se que o tratamento com PC aumentou em 52% a contagem do número de bandas em DGGE para a comunidade Archaea, em relação ao grupo MSM, sem diferir do grupo SGUM. Em linhas gerais, no presente experimento, não foi possível atribuir um padrão na estrutura de amplificação das comunidades Bacteria ou Archaea do conteúdo ruminal de animais tratados com dois diferentes modificadores ruminais ou 3 fontes energéticas distintas. / Passive immunity arises as an alternative for ruminal fermentation manipulation and aviary antibodies against specific bacteria starts to be studied. The objective of the present study was to evaluate a polyclonal antibody preparation (PAP) against Streptococus bovis, Fusobacterium necrophorum and some proteolytic bacteria (Peptostreptococcus anacrobius, Clostridium aminophilum and Clostridium sticklandii) on ruminal microbial community diversity and in situ degradability of some feedstuffs. Nine ruminally fistulated cows were used in a latin square 3 x 3 replicated 3 times with factorial arrangement of treatments 3 x 3 regarding to two rumen modifiers [monensin (MON) and (PAP) plus a control group (CON)] and three energetic sources supplemented in the diet represented by the dry-grounded corn grain (CG), high moisture corn silage (HMCS) and citrus pulp (CiPu). Each trial lasted 21 days where 16 days were for treatments adaptation and 5 for data collection. In situ degradability of the experimental diets was measured by nylon bag in situ technique. The collection of samples for quantitative protozoa analysis occurred on day 21 of each trial at 0 and 4 h after feeding by scanning the ruminal floor. The ruminal content was collected in the day 21 of each trial at 0 and 4 h after feeding for the analysis of microbial ruminal diversity by the denaturing gradient gel electrophoresis. Diets with CiPu presented an increase of 80.6%; 75.4% and 66.8% in effective degradability of NDF of sugar cane for outflow rates of 0.02, 0.05, 0.08/h, respectively, in relation to group treated with HMCS but not to the group CG. The group treated with PAP showed effect on soluble fraction (a) of starch of CG decreasing it in 45.26% and 45.37% in relation to CON and MON group respectively. It was observed that the treatment with MON decreased in 16.14% the value of potentially soluble fraction (b) of DM from HMCS in relation to CON group but not in relation to PAP. For the degradation rate (c) the MON increased it values in 63.18% and 60.65% in relation to CON and PAP group respectively. Also, MON treatment decreased potential degradability (Pd) of DM of HMCS in 3.40% in relation to CON group but not to PAP. It was observed that PAP treatment increased in 93.65% the relative counting of Isotricha in relation to CON group but not in relation to MON group. It was observed that CiPu diet increased in 334.42% (0h) and 399.75% (4h) the relative counting of Isotricha in relation to CG and HMCS. It was observed that CiPu increased in 52% the counting of the numbers of bands in DGGE for Archaea community in relation to CG without difference to HMCS group. In general lines, in the present experiment, it was not possible to assign that there was a pattern in the structures of amplification by Bacteria and Archaea communities of the ruminal content of animals treated with two different rumen modifiers or three distinct energetic sources.

Este trabalho de investigação refere-se ao uso do reator anaeróbio híbrido para tratamento de esgoto sanitário, com configuração baseada no reator anaeróbio de manta de lodo (UASB) com inclusão de: meio suporte sobre as calhas de coleta de gás (denominado reator anaeróbio híbrido - UAHB) e, também, meio suporte na zona de reação (denominado reator anaeróbio híbrido modificado - UAHBmod). Para o desenvolvimento desta pesquisa, no Campus I da USP de São Carlos-SP foram construídos dois reatores experimentais de 18,8 m3 cada: um reator UASB, com função de controle, e um reator UAHB. Primeiramente os reatores foram operados por período de 200 dias, com tempo de detenção hidráulica (TDH) de 6 h. Após serem inoculados, com 80 dias de operação, os reatores atingiram o estado de equilíbrio dinâmico aparente, com geração de alcalinidade, baixa concentração de ácidos voláteis e eficiência de remoção média de DQO, de 84% e 85% e de DBO de 87% e 91%, respectivamente para o UASB e o UAHB. Após esse período, os reatores foram submetidos a aumento da velocidade ascensional (Vasc) (mediante recirculação do efluente) de 0,78 m.h-1; 1,17 m.h-1; 1,56 m.h-1 e de 1,96 m.h-1. O UAHB mostrou ser menos susceptível ao aumento da Vasc do que o UASB. Além da análise da operação dos reatores, foram realizados os ensaios hidrodinâmicos e avaliada a estrutura da comunidade microbiana, por microscopia ótica, epifluorescência e pela técnica do DGGE. Após esse período preliminar, os reatores UAHB e UAHBmod, operados com TDH de 6h e Vasc de 0,78 m.h-1, atingiram o estado de equilíbrio dinâmico aparente, com geração de alcalinidade, baixa concentração de ácidos voláteis e eficiência de remoção média da matéria orgânica, de 71% e 76% em DQO, e de 72% e 87% em DBO, respectivamente para o UAHB e UAHBmod. Após este período, o reator UAHBmod, submetido a Vasc de 1,56 m.h-1, promoveu remoção de 74% de DQO, e de 87% de DBO. / This research refers to the use of a hybrid anaerobic reactor (UAHB) for domestic wastewater treatment. The configuration of this reactor is based on a sludge bed anaerobic reactor (UASB); in the first instance, a media support above the gas collection apparatus (also known as hybrid anaerobic reactor) was provided and later, a media support on the reaction zone (also known as hybrid modified anaerobic reactor - UAHBmod) was provided. Two reactors, with a volume of 18.8 m3, each, were built for this research at Campus I, USP in São Carlos - SP-Brazil. One UASB reactor acted as a control, and the other as a UAHB reactor. In the preliminary essays, the reactors were operated with 6h of hydraulic detention time (HDT) for 200 days. After inoculation, the reactors attained the apparent dynamic equilibrium state after 80 days of operation, with alkalinity generation, low volatile acids concentration and mean organic matter removal of 84% and 85% in terms of COD, and 87% and 91% in terms of BOD, for UASB and UAHB reactors, respectively. After this period, the reactors were submitted to an increasing in up velocity (Vup) of 0.78 m.h-1; 1.17 m.h-1; 1.56 m.h-1 and 1.96 m.h-1. The UAHB reactor showed lesser susceptibility for Vup increase than the UASB reactor. Hydrodynamic tests were also done on the reactors, in addition to routine operational analysis. The structure of the microbial community was evaluated by optical and epifluorescence microscopy, and the DGGE technique. After this step, the UAHB and the UAHBmod reactors were operated out 6h of HDT and Vup of 0.78 m.h-1. The reactors attained the apparent dynamic equilibrium state with alkalinity generation, low volatile acids concentration and mean organic matter removal of 71% and 76% in terms of COD, and 72% and 87% in terms of BOD for the UASB and UAHBmod reactors, respectively. After this period, the UAHBmod reactor was subjected to a Vup of 1.56 m.h-1 and achieved removal efficiencies of 74% COD and 87% BOD.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

In human microbiome analysis, sequencing of bacterial 16S rRNA genes has revealed a role for the gut microbiota in maintaining health and contributing to various pathologies. Novel community analysis techniques must be evaluated in terms of bias, sensitivity, and reproducibility and compared to existing techniques to be effectively implemented. Next- generation sequencing technologies offer many advantages over traditional fingerprinting methods, but this extensive evaluation required for the most efficacious use of data has not been performed previously. Illumina libraries were generated from the V3 region of the 16S rRNA gene of samples taken from 12 unique sites within the gastrointestinal tract for each of 4 individuals. Fingerprint data were generated from these samples and prominent bands were sequenced. Sequenced bands were matched with OTUs within their respective libraries. The results demonstrate that denaturing gradient gel electrophoresis (DGGE) represents relatively abundant bacterial taxa (>0.1%) beta-diversity of all samples was compared using Principal Coordinates Analysis (PCoA) of UniFrac distances and Multi-Response Permutation Procedure (MRPP) was applied to measure sample cluster strength and significance; indicator species analysis of fingerprint bands and Illumina OTUs were also compared. The results demonstrate overall similarities between community profiling methods but also indicate that sequence data were not subject to the same limitations observed with the DGGE method (i.e., only abundant taxa bands are resolved, unable to distinguish disparate samples). In addition, the effect of stochastic fluctuations in ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? differ for DGGE and next-generation sequencing. I compared pooled and individual reactions for samples of high and low template concentration for both Illumina and DGGE using the combined V3-V4 region of the 16S rRNA gene, and demonstrated that template concentration has a greater impact on reproducibility than pooling. This research shows congruity between two disparate molecular methods, identifies sources of bias, and establishes new guidelines for minimizing bias in microbial community analyses.

A imunidade passiva surge como uma alternativa para a manipulação da fermentação ruminal e anticorpos de origem aviária contra bactérias específicas começam a ser pesquisados. Objetivou-se com este trabalho avaliar um preparado de anticorpos policlonais contra Streptococus bovis, Fusobacterium necrophorum e algumas cepas de bactérias proteolíticas (Peptostreptococcus anacrobius, Clostridium aminophilum e Clostridium sticklandii) sobre a diversidade microbiana ruminal e degradabilidade in situ de alguns alimentos. Foram utilizadas nove vacas mestiças portadoras de cânula ruminal. O delineamento experimental foi o quadrado latino 3 x 3 replicado 3 vezes, com arranjo fatorial de tratamentos 3 x 3 referente a 2 modificadores ruminais representados pela monensina (MON) e pelo preparado de anticorpos policlonais (PAP) mais o grupo controle e 3 fontes energéticas suplementadas na dieta, representadas pelo milho seco moído (MSM), silagem de grão úmido de milho (SGUM) e polpa cítrica (PC). Cada subperíodo experimental foi composto de 21 dias, sendo 16 dias para adaptação aos tratamentos e 5 para coleta de dados. A degradabilidade in situ dos alimentos testados foi mensurada através da técnica de saco de náilon. A coleta de amostras para a análise quantitativa de protozoários ocorreu no 21° dia de cada período, às 0 e 4 horas pós-alimentação, sendo estas coletadas por varredura do assoalho ruminal. O conteúdo ruminal foi coletado no 21° dia de cada período, às 4 h pós-alimentação, para análise da diversidade microbiana através de técnica de eletroforese em gel com gradiente de desnaturação. Observou-se que dietas contendo PC apresentaram aumento de 80,6%; 75,4% e 66,8% da degradabilidade efetiva da FDN da cana-de-açúcar para as taxas de passagem de 2, 5, 8%/h, respectivamente, em relação ao grupo tratado com SGUM, mas não em relação ao grupo com MSM. O tratamento com PAP demonstrou efeito sobre a fração solúvel (a) do amido do MSM, diminuindo esta em 45,26% e 45,37% em relação ao grupo CON e grupo MON, respectivamente. Observou-se que o tratamento com MON diminuiu em 16,14% o valor da fração potencialmente degradável (b) da MS da SGUM em relação ao grupo CON, mas não em relação ao grupo tratado com PAP. Já sobre a taxa de degradação (c), a MON aumentou o valor desta em 63,18% e 60,65% em relação ao grupo CON e PAP, respectivamente. Também a MON diminuiu a degradabilidade potencial (Dp) da MS da SGUM em 3,40% em relação ao grupo CON, mas não em relação ao grupo tratado com PAP. Observou-se que o PAP aumentou em 93,65% a contagem relativa de Isotricha em relação ao grupo CON, mas não em relação ao grupo MON. Já a PC aumentou em 334,42% (0h) e 399,75% (4h) a contagem relativa de protozoários do gênero Isotricha em relação às dietas de MSM e SGUM. Observou-se que o tratamento com PC aumentou em 52% a contagem do número de bandas em DGGE para a comunidade Archaea, em relação ao grupo MSM, sem diferir do grupo SGUM. Em linhas gerais, no presente experimento, não foi possível atribuir um padrão na estrutura de amplificação das comunidades Bacteria ou Archaea do conteúdo ruminal de animais tratados com dois diferentes modificadores ruminais ou 3 fontes energéticas distintas. / Passive immunity arises as an alternative for ruminal fermentation manipulation and aviary antibodies against specific bacteria starts to be studied. The objective of the present study was to evaluate a polyclonal antibody preparation (PAP) against Streptococus bovis, Fusobacterium necrophorum and some proteolytic bacteria (Peptostreptococcus anacrobius, Clostridium aminophilum and Clostridium sticklandii) on ruminal microbial community diversity and in situ degradability of some feedstuffs. Nine ruminally fistulated cows were used in a latin square 3 x 3 replicated 3 times with factorial arrangement of treatments 3 x 3 regarding to two rumen modifiers [monensin (MON) and (PAP) plus a control group (CON)] and three energetic sources supplemented in the diet represented by the dry-grounded corn grain (CG), high moisture corn silage (HMCS) and citrus pulp (CiPu). Each trial lasted 21 days where 16 days were for treatments adaptation and 5 for data collection. In situ degradability of the experimental diets was measured by nylon bag in situ technique. The collection of samples for quantitative protozoa analysis occurred on day 21 of each trial at 0 and 4 h after feeding by scanning the ruminal floor. The ruminal content was collected in the day 21 of each trial at 0 and 4 h after feeding for the analysis of microbial ruminal diversity by the denaturing gradient gel electrophoresis. Diets with CiPu presented an increase of 80.6%; 75.4% and 66.8% in effective degradability of NDF of sugar cane for outflow rates of 0.02, 0.05, 0.08/h, respectively, in relation to group treated with HMCS but not to the group CG. The group treated with PAP showed effect on soluble fraction (a) of starch of CG decreasing it in 45.26% and 45.37% in relation to CON and MON group respectively. It was observed that the treatment with MON decreased in 16.14% the value of potentially soluble fraction (b) of DM from HMCS in relation to CON group but not in relation to PAP. For the degradation rate (c) the MON increased it values in 63.18% and 60.65% in relation to CON and PAP group respectively. Also, MON treatment decreased potential degradability (Pd) of DM of HMCS in 3.40% in relation to CON group but not to PAP. It was observed that PAP treatment increased in 93.65% the relative counting of Isotricha in relation to CON group but not in relation to MON group. It was observed that CiPu diet increased in 334.42% (0h) and 399.75% (4h) the relative counting of Isotricha in relation to CG and HMCS. It was observed that CiPu increased in 52% the counting of the numbers of bands in DGGE for Archaea community in relation to CG without difference to HMCS group. In general lines, in the present experiment, it was not possible to assign that there was a pattern in the structures of amplification by Bacteria and Archaea communities of the ruminal content of animals treated with two different rumen modifiers or three distinct energetic sources.

Este trabalho de investigação refere-se ao uso do reator anaeróbio híbrido para tratamento de esgoto sanitário, com configuração baseada no reator anaeróbio de manta de lodo (UASB) com inclusão de: meio suporte sobre as calhas de coleta de gás (denominado reator anaeróbio híbrido - UAHB) e, também, meio suporte na zona de reação (denominado reator anaeróbio híbrido modificado - UAHBmod). Para o desenvolvimento desta pesquisa, no Campus I da USP de São Carlos-SP foram construídos dois reatores experimentais de 18,8 m3 cada: um reator UASB, com função de controle, e um reator UAHB. Primeiramente os reatores foram operados por período de 200 dias, com tempo de detenção hidráulica (TDH) de 6 h. Após serem inoculados, com 80 dias de operação, os reatores atingiram o estado de equilíbrio dinâmico aparente, com geração de alcalinidade, baixa concentração de ácidos voláteis e eficiência de remoção média de DQO, de 84% e 85% e de DBO de 87% e 91%, respectivamente para o UASB e o UAHB. Após esse período, os reatores foram submetidos a aumento da velocidade ascensional (Vasc) (mediante recirculação do efluente) de 0,78 m.h-1; 1,17 m.h-1; 1,56 m.h-1 e de 1,96 m.h-1. O UAHB mostrou ser menos susceptível ao aumento da Vasc do que o UASB. Além da análise da operação dos reatores, foram realizados os ensaios hidrodinâmicos e avaliada a estrutura da comunidade microbiana, por microscopia ótica, epifluorescência e pela técnica do DGGE. Após esse período preliminar, os reatores UAHB e UAHBmod, operados com TDH de 6h e Vasc de 0,78 m.h-1, atingiram o estado de equilíbrio dinâmico aparente, com geração de alcalinidade, baixa concentração de ácidos voláteis e eficiência de remoção média da matéria orgânica, de 71% e 76% em DQO, e de 72% e 87% em DBO, respectivamente para o UAHB e UAHBmod. Após este período, o reator UAHBmod, submetido a Vasc de 1,56 m.h-1, promoveu remoção de 74% de DQO, e de 87% de DBO. / This research refers to the use of a hybrid anaerobic reactor (UAHB) for domestic wastewater treatment. The configuration of this reactor is based on a sludge bed anaerobic reactor (UASB); in the first instance, a media support above the gas collection apparatus (also known as hybrid anaerobic reactor) was provided and later, a media support on the reaction zone (also known as hybrid modified anaerobic reactor - UAHBmod) was provided. Two reactors, with a volume of 18.8 m3, each, were built for this research at Campus I, USP in São Carlos - SP-Brazil. One UASB reactor acted as a control, and the other as a UAHB reactor. In the preliminary essays, the reactors were operated with 6h of hydraulic detention time (HDT) for 200 days. After inoculation, the reactors attained the apparent dynamic equilibrium state after 80 days of operation, with alkalinity generation, low volatile acids concentration and mean organic matter removal of 84% and 85% in terms of COD, and 87% and 91% in terms of BOD, for UASB and UAHB reactors, respectively. After this period, the reactors were submitted to an increasing in up velocity (Vup) of 0.78 m.h-1; 1.17 m.h-1; 1.56 m.h-1 and 1.96 m.h-1. The UAHB reactor showed lesser susceptibility for Vup increase than the UASB reactor. Hydrodynamic tests were also done on the reactors, in addition to routine operational analysis. The structure of the microbial community was evaluated by optical and epifluorescence microscopy, and the DGGE technique. After this step, the UAHB and the UAHBmod reactors were operated out 6h of HDT and Vup of 0.78 m.h-1. The reactors attained the apparent dynamic equilibrium state with alkalinity generation, low volatile acids concentration and mean organic matter removal of 71% and 76% in terms of COD, and 72% and 87% in terms of BOD for the UASB and UAHBmod reactors, respectively. After this period, the UAHBmod reactor was subjected to a Vup of 1.56 m.h-1 and achieved removal efficiencies of 74% COD and 87% BOD.