Non-alcoholic fatty liver disease (NAFLD) includes simple hepatic steatosis (SS) and non-alcoholic steatohepatitis (NASH). NAFLD is tightly linked to obesity and is thought to be secondary to various noxious signals, some of which may originate from the intestinal microbiota (IM). Despite a growing body of evidence supporting a link between obesity and altered IM, there are no studies assessing the IM of patients with NAFLD. In this cross-sectional study we aimed at comparing fecal levels of total bacteria, Bacteroidetes, C. coccoides, C. leptum, Bifidobacteria, E. coli, and Archaea between healthy controls (HC) and patients with SS or NASH. We found higher C. coccoides levels in NASH compared to SS and lower percentage Bacteroidetes in NASH compared to SS and HC. Controlling for body mass index and fat intake we found an association between presence of NASH and percentage Bacteroidetes. The latter inversely correlated with insulin resistance.

Non-alcoholic fatty liver disease (NAFLD) includes simple hepatic steatosis (SS) and non-alcoholic steatohepatitis (NASH). NAFLD is tightly linked to obesity and is thought to be secondary to various noxious signals, some of which may originate from the intestinal microbiota (IM). Despite a growing body of evidence supporting a link between obesity and altered IM, there are no studies assessing the IM of patients with NAFLD. In this cross-sectional study we aimed at comparing fecal levels of total bacteria, Bacteroidetes, C. coccoides, C. leptum, Bifidobacteria, E. coli, and Archaea between healthy controls (HC) and patients with SS or NASH. We found higher C. coccoides levels in NASH compared to SS and lower percentage Bacteroidetes in NASH compared to SS and HC. Controlling for body mass index and fat intake we found an association between presence of NASH and percentage Bacteroidetes. The latter inversely correlated with insulin resistance.

The collection of microbes that inhabits the human gastrointestinal tract is known as intestinal microbiota, and an enormous body of work has shown that their activities contribute to health and disease. Ulcerative colitis (UC), which is a type of inflammatory bowel disease, is considered to arise due to a disruption in the balance between the immune system and microbiota. However, there is little consensus on the mechanism of action and microbes involved in the disease manifestation. In this work, I applied culture-enriched metagenomics (CEMG) to characterize the dynamics of gut microbiota in healthy individuals and UC patients. I showed that CEMG provides a higher resolution to study these microbial communities, and we used this approach to understand microbial colonization after fecal microbiota transplantation (FMT) therapy in UC patient. I showed that sequencing approaches alone did not reveal consistent engraftment across FMT responders. Using CEMG and a collection of bacterial whole-genome sequences, I showed patient-specific microbial strain transfer and a signature of commonly engrafted genes only in patients who responded to FMT. In this work, I also investigated the dynamics of a highly abundant bacteriophage, crAssphage, in an FMT donor and implemented a new method to detect bacteriophage engraftment post-FMT using SNP analysis. Finally, it has been suggested that antibiotic treatment before FMT may increase the efficacy of FMT. However, in this work, I show that while antibiotics alter the microbiome, there was no difference in the composition of the microbiome of antibiotic vs placebo group post-FMT. This is consistent with the randomized controlled trial results that shows pretreatment with antibiotics does not improve FMT outcome. Together, this work demonstrate the importance of in-depth microbiome analysis applied to culture-dependent and -independent sequencing to characterize microbial changes post-FMT. / Dissertation / Doctor of Philosophy (PhD) / Many bacteria reside in the human gut, and they are essential in our health and in disease. It is evident that these bacteria are associated with inflammatory bowel disease, but we do not yet know how and what bacteria are involved in this disease. In this work, I describe a method to study these bacteria from stool that relies on growing them and investigating their DNA. I showed that our approach helped us recover a greater diversity of these bacteria and their genetic content in healthy individuals and patients with inflammatory bowel disease compared to methods that use only DNA based approaches. Using this method, we could better understand why some patients responded to a treatment consisting of transferring stool content from healthy donor to patient. I also investigated a group of viruses that infect bacteria and implemented a new computational method based on DNA sequencing to test whether these viruses transfer to the patient after receiving the fecal therapy. We also found that antibiotic treatment before fecal therapy in patients with inflammatory bowel disease does not improve the patient’s recovery.

A microbiota intestinal humana é um ecossistema complexo que abriga centenas de espécies bacterianas e que de um modo geral convive harmonicamente com o hospedeiro. Essa interação promove o desenvolvimento e estimulação do sistema imune. A microbiota tem papel primordial na saúde humana por produzir nutrientes, participar no metabolismo de carboidratos e por competir com bactérias patogênicas na colonização do ambiente intestinal. Ela alcança sua estabilidade em torno do segundo ano de vida. O tipo de parto, de alimentação, as condições sanitárias, sociais e os elementos do hospedeiro, como fatores genéticos, peristaltismo e pH intestinal, influenciam na sua composição. Quando há a instalação de infecções intestinais ou uso de antimicrobianos e de imunossupressores ocorre o desequilíbrio desse sistema. Esse estudo tem como objetivo avaliar o estabelecimento e a diversidade da microbiota intestinal em onze crianças a partir do segundo dia até o décimo segundo mês de vida. As amostras fecais das crianças foram coletadas no segundo e sétimo dias de vida e mensalmente do primeiro ao décimo segundo meses de vida. As análises de \"fingerprinting\" foram realizadas pelo método de eletroforese em gel com gradiente desnaturante (DGGE) usando os iniciadores para a região V3 do gene 16S rRNA. Os perfis de similaridade foram feitos a partir da construção de dendrogramas e para avaliar as relações entre as amostras temporais das crianças e o perfil de bandas obtido com o DGGE foram feitas análises de correspondência. A análise do \"fingerprinting\" mostrou que cada criança apresentou um padrão de colonização distinto. Apesar de compartilharem algumas características como a forma de nascimento, quadro sócio-econômico e terem condições sanitárias semelhantes, observaram-se diferenças no processo de estabelecimento da microbiota de cada uma delas, o que pode ser devido aos fatores individuais e particularidades da alimentação, do uso de medicamentos e das intercorrências infecciosas. As análises de correspondência mostraram agrupamentos temporais, onde as amostras mais tardias (a partir de 10 meses até 12 meses de idade) estão muito relacionadas entre si indicando o início da estabilização da microbiota ao final do 1º ano de vida. O uso da técnica de \"fingerprinting\" por DGGE permitiu uma análise global dos estágios diferentes no estabelecimento da microbiota intestinal. / The human intestinal microbiota is a complex ecosystem that homes hundreds of bacterial species, which generally live in harmony with the host. This interaction promotes the development and stimulation of the immune system. The microbiota plays a major role in human health by producing nutrient involved in carbohydrate metabolism and competes with pathogenic bacteria in the colonization of the intestinal environment. The stability is achieved around the second year of life. The type of delivery, food, sanitation, and social elements of the host, such as genetic factors, peristaltism and intestinal pH, influence their composition. The imbalance of this system happens due the installation of intestinal infections, in the use of antibiotics and immunosuppressants. The aim of this study is to evaluate the establishment and the diversity of the intestinal microbiota of eleven children from the second day of life until the twelfth month of life. The fecal samples were collected from children in the second and seventh days of life and monthly from the first month to the twelfth month of life. Analyses of fingerprinting was performed by the method of denaturing gradient gel electrophoresis (DGGE) using the primers for the V3 region of the 16S rRNA gene. The similarity profiles were made with the construction of dendrograms and to evaluate the relationships between the temporal samples of children and the profile obtained from the DGGE bands were made the correspondence analysis (CA). The fingerprinting analysis showed that each child had a distinct pattern of bands. Although sharing some characteristics such as delivery mode, socio-economic context and similar health conditions were observed differences in the process of establishment of the microbiota of each, which may be due to individual factors, the use of medicine and infectious complications. The correspondence analysis showed temporal clusters, where the later samples (from 10 months to 12 months of age) are closely related to each other indicating the beginning of the stabilization of the microbiota at the end of the first year of life. Using the technique of fingerprintin by DGGE allowed a comprehensive analysis of different stages in the intestinal microbiota establishment.

Two different feeding trials were conducted to evaluate the effects of dietary supplementation with the dairy/yeast prebiotic GroBiotic-A (GBA) to Nile tilapia diets. A nutritionally complete basal diet was supplemented with GBA at either 1 or 2% of dry weight, and all three diets were fed to triplicate groups of juvenile fish in two consecutive trials. Trial 1 continued for 8 weeks, while Trial 2 was conducted for 5 weeks to more specifically assess immunological responses, intestinal characteristics and disease resistance of tilapia. At the conclusion of Trial 1, there were no differences in weight gain (WG) or feed efficiency (FE) among fish fed the three diets. However, fish fed the diet with GBA at 2% had significantly increased survival and noticeably elevated levels of plasma lysozyme compared to fish fed the basal diet or the diet with GBA at 1%. Similarly, at the conclusion of Trial 2, WG and FE were unaffected by GBA supplementation; however, fish fed the diet with GBA at 2% also exhibited elevated plasma lysozyme as well as significantly (P < 0.05) increased levels of extracellular superoxide anion production (EX-SOAP) by macrophages. Dendrogram analysis of denaturing gradient gel electrophoresis (DGGE) images detected a significantly different microbial community within the intestine of fish fed the diet with GBA at 2% compared to fish fed the basal diet and diet with GBA at 1%. None of the experimental diets resulted in significant improvements to survival after exposure to Streptococcus iniae due to within treatment variability. However, fish fed the diet with GBA at 2% did tend to experience reduced mortality (12.5%) as compared to fish fed the basal diet (35%). Thus, supplementation of GBA at 2% of diet did alter the gut microbiota of tilapia and enhanced immunological responses and disease resistance to S. iniae.

There has been a rapid increase in the number of overweight and obese individuals worldwide in the past 50 years. It has been assumed that an increased caloric intake and a more sedentary lifestyle are the main causes of this rise. However, recent evidence has shown that the microbes that live in the human gastrointestinal tract may play a role in the regulation of weight and obesity development. These microbes, termed the gut microbiota, are commensal and symbiotic microbes that are densely populated throughout an individual's gastrointestinal tract. This paper presents the relevant research and possible mechanisms of how these microbes, mainly bacteria, are thought to play a role in weight regulation and obesity.

Made available in DSpace on 2014-06-11T19:31:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2003Bitstream added on 2014-06-13T19:41:23Z : No. of bitstreams: 1 monreal_mtfd_dr_botfm.pdf: 1555649 bytes, checksum: 0bf7e0b05dcf2f4d0b89f10dce0efb02 (MD5) / O trato gastrointestinal possui enorme variedade de bactérias aeróbias e anaeróbias, metabolicamente ativas, que interagem entre si em complexo ecossistema. Essa microbiota desempenha funções importantes no metabolismo, nutrição, imunidade e proteção contra a colonização por microrganismos patogênicos. Vários fatores podem influenciar essa microbiota, entre eles a idade, dieta, processos inflamatórios e infecciosos e utilização de antimicrobianos. Assim, este estudo foi desenvolvido com o objetivo de verificar a influência das infecções bacterianas do trato respiratório e do tratamento com amoxicilina sobre a microbiota intestinal normal do paciente. O processo infeccioso bacteriano do trato respiratório influenciou a microbiota intestinal dos pacientes. Houve redução significativa na quantidade de UFC/g de fezes de microrganismos dos gêneros Bacteroides e Lactobacillus. A utilização de amoxicilina também influenciou a microbiota intestinal. Foi observada redução significativa na quantidade de UFC/g de fezes de microrganismos dos gêneros Bifidobacterium e Lactobacillus. É importante identificar modificações na composição da microbiota intestinal, uma vez que a diminuição destes microrganismos pode representar diversos prejuízos para o hospedeiro. Um destes prejuízos é a diminuição da resistência à colonização. Esses prejuízos, quando acompanhados, podem ser minimizados pela equipe de saúde por meio de medidas relativas à conduta terapêutica e alimentar, visando reduzir a influência nociva sobre o ecossistema gastrointestinal. / The gastrointestinal tract contains an enormous variety of metabolically active aerobic and anaerobic bacteria, that interact with each other in a complex ecosystem. That microbiota carries out important functions in the metabolism, nutrition, immunity and protection against the colonization by pathogenic microorganisms. Several factors can influence this microbiota, among them are age, diet, inflammatory and infectious processes and use of antimicrobial agents. Thus, this study was developed with the objective of verifying the influence of the bacterial infections of the respiratory tract and of the treatment using amoxicillin on the patient's normal intestinal microbiota. The bacterial infectious process of the respiratory tract influenced the patients' intestinal microbiota. There was significant reduction in the amount of CFU/g of feces of microorganisms of the Bacteroides and Lactobacillus genus. The use of amoxicillin also influenced the intestinal microbiota. Significant reduction was observed in the amount of CFU/g of feces of microorganisms of the Bifidobacterium and Lactobacillus genus. It is important to identify modifications in the composition of the intestinal microbiota, once the decrease of these microorganisms can cause damage to the host. One of these damages is the decrease in the resistance to the colonization. Those damages, when accompanied, can be minimized by the health staff using measures related to the therapeutic and alimentary conduct, seeking to reduce the noxious influence on the gastrointestinal ecosystem.

Made available in DSpace on 2014-06-11T19:27:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-04-16Bitstream added on 2014-06-13T19:35:50Z : No. of bitstreams: 1 souza_me_me_botfm.pdf: 389941 bytes, checksum: 22df6f35de73f9795005298ac7945965 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Universidade Estadual Paulista (UNESP) / A microbiota intestinal normal embora bastante estável pode se alterar em condições patológicas, modificações na composição da dieta, presença de distúrbios gastrointestinais e/ou ingestão de drogas. A associação de infecção com a utilização de medicamentos dificulta a interpretação da participação desses fatores na microbiota intestinal. O objetivo do presente estudo foi avaliar a microbiota intestinal de indivíduos que sofreram acidente ocupacional com materiais biológicos e receberam anti-retrovirais. Foram estudados 23 indivíduos adultos com idade entre 18-45 anos, sendo 13 doadores de sangue, grupo controle (GC) e 10 que sofreram acidente ocupacional com material biológico e realizaram profilaxia anti-retroviral. Foram avaliados a microbiota intestinal, medidas antropométricas, exames laboratoriais (hemograma, função renal, hepática, lipidograma, glicemia, proteínas totais e frações) pré, após a medicação e 30 dias após o término da medicação. A zidovudina mais a lamivudina foi utilizada em 70% dos indivíduos associado ao nelfinavir, 20% ao efavirenz e 10% ao ritonavir. Náuseas, vômitos e diarréia estiveram presentes em 80% no segundo momento do estudo. Sobrepeso em 70%, desnutrição e eutrofia em 10%, dos indivíduos sem alteração durante o estudo. As enzimas AST, ALT, Gama-GT e triglicérides, LOL-colesterol se elevaram no segundo momento e se normalizaram 30 dias após término da medicação. Foi observada redução significativa dos três gêneros de bactérias anaeróbias avaliadas Lacfobacillus , Bifidobacferium e Bacleróides em relação ao grupo controle nos três momentos. O uso de anti-retrovirais provocou impacto significativo na microbiota intestinal dos indivíduos normais em uso de anti-retrovirais, não sendo recuperada 30 dias após o término da medicação. / Pathological conditions, changes in diet composition, presence of gastrointestinal disorders and/or ingestion of drugs may alter the normal intestinal microbiota, regardless of its sufficient steadiness. The association of infection with the use of medicine makes the interpretation of the participation of these factors in intestinal microbiota difficult. The objective of the present study was to evaluate the intestinal microbiota from individuais injured by biological materiais in occupational accident, submitied to antiretroviral prophylaxis. 23 adult individuais with ages between 18-45 years old were studied, being 13 blood donors (control group - CG) and 10 individuais injured by biological materiais in occupational accident, submitled to antiretroviral prophylaxis. Intestinal microbiota, anthropometric measures and biochemical examinations (blood count, renal and hepatic functions, glucose and lipids blood levels, total proteins and fractions) were evaluated before, right after and 30 days after the end of medication. Zidovudine plus lamivudine were used in 70% of the individuais associated to nelfinavir, 20% to efavirenz and 10% to ritonavir. Nausea, vomiting and cliarrhea were present in 80% of the individuais at the second part of the study. Overweight was noticed in 70% and malnutrition anel eutrophia were noticed in 10% of the individuais without alterations during the study. AST, ALT, Gamma-GT and triglycerides and LDL-cholesterol enzymes were increased at the second part and normalized 30 days after the end of medication. Significant reduction of the three genera of anaerobic bacteria - Lactobacil/us, Bifidobacterium and Bacteroides - evaluated was observed in reiation to the controi group at the three moments. The use of antiretrovirals caused significant impact in the intestinal microbiota of the normal individuais, without recovery 30 days after the end of medication.

A microbiota intestinal humana é um ecossistema complexo que abriga centenas de espécies bacterianas e que de um modo geral convive harmonicamente com o hospedeiro. Essa interação promove o desenvolvimento e estimulação do sistema imune. A microbiota tem papel primordial na saúde humana por produzir nutrientes, participar no metabolismo de carboidratos e por competir com bactérias patogênicas na colonização do ambiente intestinal. Ela alcança sua estabilidade em torno do segundo ano de vida. O tipo de parto, de alimentação, as condições sanitárias, sociais e os elementos do hospedeiro, como fatores genéticos, peristaltismo e pH intestinal, influenciam na sua composição. Quando há a instalação de infecções intestinais ou uso de antimicrobianos e de imunossupressores ocorre o desequilíbrio desse sistema. Esse estudo tem como objetivo avaliar o estabelecimento e a diversidade da microbiota intestinal em onze crianças a partir do segundo dia até o décimo segundo mês de vida. As amostras fecais das crianças foram coletadas no segundo e sétimo dias de vida e mensalmente do primeiro ao décimo segundo meses de vida. As análises de \"fingerprinting\" foram realizadas pelo método de eletroforese em gel com gradiente desnaturante (DGGE) usando os iniciadores para a região V3 do gene 16S rRNA. Os perfis de similaridade foram feitos a partir da construção de dendrogramas e para avaliar as relações entre as amostras temporais das crianças e o perfil de bandas obtido com o DGGE foram feitas análises de correspondência. A análise do \"fingerprinting\" mostrou que cada criança apresentou um padrão de colonização distinto. Apesar de compartilharem algumas características como a forma de nascimento, quadro sócio-econômico e terem condições sanitárias semelhantes, observaram-se diferenças no processo de estabelecimento da microbiota de cada uma delas, o que pode ser devido aos fatores individuais e particularidades da alimentação, do uso de medicamentos e das intercorrências infecciosas. As análises de correspondência mostraram agrupamentos temporais, onde as amostras mais tardias (a partir de 10 meses até 12 meses de idade) estão muito relacionadas entre si indicando o início da estabilização da microbiota ao final do 1º ano de vida. O uso da técnica de \"fingerprinting\" por DGGE permitiu uma análise global dos estágios diferentes no estabelecimento da microbiota intestinal. / The human intestinal microbiota is a complex ecosystem that homes hundreds of bacterial species, which generally live in harmony with the host. This interaction promotes the development and stimulation of the immune system. The microbiota plays a major role in human health by producing nutrient involved in carbohydrate metabolism and competes with pathogenic bacteria in the colonization of the intestinal environment. The stability is achieved around the second year of life. The type of delivery, food, sanitation, and social elements of the host, such as genetic factors, peristaltism and intestinal pH, influence their composition. The imbalance of this system happens due the installation of intestinal infections, in the use of antibiotics and immunosuppressants. The aim of this study is to evaluate the establishment and the diversity of the intestinal microbiota of eleven children from the second day of life until the twelfth month of life. The fecal samples were collected from children in the second and seventh days of life and monthly from the first month to the twelfth month of life. Analyses of fingerprinting was performed by the method of denaturing gradient gel electrophoresis (DGGE) using the primers for the V3 region of the 16S rRNA gene. The similarity profiles were made with the construction of dendrograms and to evaluate the relationships between the temporal samples of children and the profile obtained from the DGGE bands were made the correspondence analysis (CA). The fingerprinting analysis showed that each child had a distinct pattern of bands. Although sharing some characteristics such as delivery mode, socio-economic context and similar health conditions were observed differences in the process of establishment of the microbiota of each, which may be due to individual factors, the use of medicine and infectious complications. The correspondence analysis showed temporal clusters, where the later samples (from 10 months to 12 months of age) are closely related to each other indicating the beginning of the stabilization of the microbiota at the end of the first year of life. Using the technique of fingerprintin by DGGE allowed a comprehensive analysis of different stages in the intestinal microbiota establishment.

Inflammatory bowel disease (IBD) is a growing disorder with unknown etiology. However, increasing evidence strongly highlights the role of gut microbiota with possible involvement of microbial plasmidome in the inflammatory process. Although the composition of the gut microbiota has been extensively studied, important functional groups such as butyrate producers remain poorly characterized, particularly in pediatric IBD. Furthermore, evaluation of the gut plasmidome in healthy and IBD children is missing. In this study, we used molecular techniques involving quantitative PCR (qPCR) and next-generation sequencing of functional and 16S rRNA genes to analyze the level and composition of butyrate-producing microbes in mucosal washes collected from the right colon of healthy children and Crohn's disease (CD) patients during diagnostic colonoscopy. Also, we isolated and characterized the gut plasmidome from the right colon mucosal washes collected from pediatric non-IBD control, ulcerative colitis (UC), and CD subjects. Although no difference was observed in the total amount of butyrate producers that utilize the butyrate kinase (BUK) pathway for butyrate synthesis, butyrate producers that use the butyryl CoA:acetate CoA-transferase (BCoAT) pathway were decreased in CD patients with inflamed colon as compared to controls. This functional gene approach shows that pediatric CD is characterized by generalized decreased abundance of Eubacterium rectale and increased abundance of Faecalibacterium prausnitzii in patients with inflamed colon. Also, phylogenetic analysis highlighted 15 Operational Taxonomic Units (OTUs) as potential novel butyrate producers, five of which were decreased in CD patients. Using 16S rRNA sequencing approach validated the functional gene results and showed decreased abundance of Coprococcus in CD patients with inflamed colon. Furthermore, non-IBD plasmidome has higher level of genes involved in butyrate synthesis and regulation of different cellular processes and stress response. On the other hand, IBD plasmidome is enriched with antibiotic resistance genes and phage elements, and pediatric CD plasmidome in particular has higher abundance of the adenosine-5'-phosphosulfate reductase gene. Altogether, our study represents the first comprehensive description of gut butyrate producers and plasmidome of pediatric subjects that emphasize a characteristic dysbiosis of butyrate producers in pediatric CD and a potential link between the gut plasmidome and IBD pathogenesis.