Calif., Univ. of California, Diss.--Los Angeles, 2002. / Kopie, ersch. im Verl. UMI, Ann Arbor, Mich. - Enth. 3 Beitr.

Univ., Diss.--Osnabrück, 1999.

Une consommation élevée de sel a été associée à beaucoup de maladies et à un risque accru de décès. Plusieurs mécanismes sous-jacents, y compris le stress oxydatif, ont été étudiés. Mais la salinité dans l'intestin et l'altération possiblement associée de son microbiote, récemment identifiées comme un symbiote critique de la santé et de la maladie, n'ont pas encore été explorées chez l'homme. En testant 1334 prélèvements de selles, nous avons montré qu'une salinité élevée était associée à une diminution de la diversité globale et à l'émergence de populations microbiennes halophiles dans l'intestin. La salinité fécale était associée au régime alimentaire salé et à l'obésité, conformément aux données épidémiologiques. Aucun procaryote halophile n’a été cultivé en dessous d'un seuil de salinité fécale de 1,5 %. Au-delà de ce seuil, nous avons découvert une diversité inattendue de microbiote halophile humain dont la richesse était corrélée avec les concentrations de sel; 64 espèces différentes ont été isolées, dont 21 nouvelles espèces et 43 espèces connues dans l'environnement mais non chez les humains. Trois procaryotes extrêmement halophiles ont été isolés, dont deux Archaea appartenant au genre Haloferax, avec une nouvelle espèce Haloferax massiliensis, et un nouveau genre bactérien, Halophilibacterium massiliense. D'autres études devraient spécifier les facteurs qui conduisent à la salinité intestinale et préciser si les altérations de microbiota intestinal associées à des niveaux élevés de sel peuvent être liées à des causes humaines / High salt intake has been linked with many diseases and an increased risk of death. Several underlying mechanisms, including oxidative stress, have been investigated, but salinity in human gut and the possible associated alteration of its microbiota recently identified as a critical symbiote of health and disease, have not yet been investigated in humans. Here, by testing 1,334 stools, we have shown that high salinity is associated with a decrease in overall diversity but the emergence of halophilic microbial populations in the intestine. Fecal salinity was associated with saline diet and obesity, according to epidemiological data. No halophilic prokaryote can be grown below a fecal salinity threshold of 1.5%. Beyond this threshold, we discovered an unexpected diversity of human cultured halophilic microbiota whose richness was correlated with salt concentrations; 64 different species were isolated, including 21 new unknown species and 43 known species in the environment but not in humans. Three extremely halophilic prokaryotes were isolated, including two Archaea belonging to the genus Haloferax, with a new species Haloferax massiliensis, and a new bacterial genus, Halophilibacteriums massiliense. Further studies should specify the factors driving gut salinity, and clarify if the gut microbiota alterations associated with high salt levels could be causally related to human diseas

Transposons are selfish, mobile genetic elements, moving within the genome. The transposase genemakes this possible, as it codes for the enzyme that catalyzes the movement. In the case of bacteria,they can also move horizontally between individual bacteria, and sometimes even between species.By default, they are a burden for the host organism, coding for a protein that the host does not need.They also pose the risk of disabling the host’s crucial genes by inserting themselves into it.Transposons are under some pressure to benefit the host, to help propagate themselves moreeffectively. And some transposons have indeed evolved to benefit the host. Lactobacillus kunkeei is a bacterial species known to reside in honeybee guts. It is known for itsrole in honey preservation and wine spoilage. The genome of L. kunkeei is reduced because it is asymbiont, however it contains an unusually high amount of transposons in its genome. In this study, the transposase genes (transposon enzymes) found in L. kunkeei are studied andcategorized. The L. kunkeei have been extracted from honeybees (Apis mellifera). The honeybeesthemselves have been collected from the islands Åland and Gotland. This study focuses on the transposase genes that come in pairs, one after another in the genome.Transposase genes were identified using annotation software and orthology-based methods. Theannotation software provides numbering for the genes, which allows finding paired genes. Thepaired genes were categorized based on alignments and phylogenetic software. Pseudogenizedtransposons were identified based on length and/or clustering into triplets. A total of 766 paired transposase genes were found. The transposase genes were found to take up1.9% of the genome, on average. A low level of diversity has been found when performingalignments and generating phylogenetic trees. The positions of the transposase genes are generallyconserved within phylogenetic groups. Pseudogenization has been detected for some transposasegenes – 4.5 per genome, on average. All of the studied transposons belong to the IS3 family, whichis a family of Class I transposons.

Earthworm-microbial interactions with emphasis on the passage effects of Eisenia spp. on microbial community were investigated. The study was focused on earthworm potential to regulate functional microbiota in cattle-impacted soils. Microbial communities were studied through a combination of polar lipid analyses, molecular, and culturing methods.

As limitações ao uso de antibióticos promotores de crescimento vêm aumentando a procura por aditivos substitutos para manter a performance animal, a saúde intestinal e a resposta imune de frangos de corte. Este experimento foi conduzido para comparar o efeito e a dose resposta do produto Ava Cid P (composto por substância húmica, butirato de sódio 30% protegido e uma pequena porção de acidificantes) suplementado na dieta, sobre a performance, resposta imune e saúde intestinal de frangos de corte. O experimento seguiu um design inteiramente casualizado, envolvendo um arranjo fatorial 2 x 5 (2 sexos e 5 tratamentos) com 7 repetições de 15 aves por tratamento. Os tratamentos seguiram a suplementação em diferentes fases de 1 a 49 dias: 1) Controle: dieta basal sem nenhuma suplementação; 2) AVA1-21: aves receberam 0,91 kg/t de Ava Cid P de 1 a 21 d; 3) AVA1-35: 0,91 kg/t de Ava Cid P de 1-21 d e 0,45 kg/t de 22-35 d; 4) AVA1-42: 0,91 kg/t de Ava Cid P de 1 a 21 d e 0,45 kg/t de 22- 42 d; 5) AVA1-49: 0,91 kg/t de Ava Cid P de 1 a 21 d, 0,45 kg/t de 22-35 d e 0,23 kg/t de 36-49 d. A suplementação com Ava Cid P não influenciou a performance de machos e fêmeas, nem mesmo a densidade de células caliciformes (P > 0,05). No entanto, o Ava Cid P foi capaz de modificar a morfometria intestinal, aumentando a altura de vilosidades aos 9 e 35 d (P < 0,05). A área superficial aparente dos vilos e altura de vilos, nas aves que receberam Ava Cid P durante todas as fases experimentais, foi superior à das aves suplementadas somente na fase inicial. No íleo, a área superficial aparente dos vilos também foi superior nas aves suplementadas aos 9 d. Além disso, a expressão do gene para mucina 2 (MUC2) e para o fator de necrose tumoral (TNF-α) diminuiu nas aves recebendo Ava Cid P aos 21 d (P < 0,05), mas não foram observadas diferenças estatísticas para interleucina-1 beta e interleucina-10. Os resultados sugerem que Ava Cid P pode alterar a expressão de mRNA de algumas citocinas e MUC2 e a morfometria intestinal de frangos de corte, aumentando a superfície aparente e a altura dos vilos, o que demonstra a potencialidade do produto como alternativa aos antibióticos promotores de crescimento. / The limitations of the antibiotic growth promoter’s (AGP) usage have been increasing the search for new products to improve poultry performance, gut healthy and immune response. This experiment was conducted to compare the effect and dose response of Ava Cid P (consisted of a humic substance, coated sodium butyrate 30% and a small acidifier portion) diet supplementation on performance, immune response and gut health of broilers. Five dietary regimens were used: 1) birds didn’t receive Ava Cid P in any phase (Control), 2) birds received 0.91 kg/t of Ava Cid P from 1 to 21 d (AVA1-21), 3) 0.91 kg/t of Ava Cid P from 1 to 21 d and 0.45 kg/t from 22 to 35 d (AVA1-35), 4) 0.91 kg/t of Ava Cid P from 1 to 21 d and 0.45 kg/t from 22 to 42 d (AVA1-42), 5) 0.91 kg/t of Ava Cid P from 1 to 21 d, 0.45 kg/t from 22 to 35 d and 0.23 kg/t from 36 to 49 d (AVA1-49). They were applied in a completely randomized design, involving a 2 × 5 factorial arrangement with 2 sex and 5 levels of inclusion, and 7 replications with 15 birds each. The supplementation with Ava Cid P showed no influence on males and females growth performance and goblet cell density (P > 0.05). However, it modified the gut morphometry, increasing jejunum villi height at 9 and 35 days (P < 0.05). The apparent villus surface area and villi height on birds fed with Ava Cid P during all phases also increased in relation to those who received only in the early phase. The expression of mucin 2 (MUC2) and tumor necrosis factor-alpha (TNF-α) decreased on birds that received Ava Cid P at 21 days (P < 0.05), but no differences were seen for interleukin-1beta (IL-1β) and interleukin-10 (IL-10). The results suggest that Ava Cid P can alter the mRNA expression of some inter-leukins, MUC2 and intestinal morphometry in broilers, increasing apparent villus surface area and villi height, which demonstrates the product potential as an alternative growth promoter.

Introdução: O trato gastrointestinal humano é composto por uma comunidade microbiana diversificada que atua no controle da saúde. Estudos recentes demonstraram que o equilíbrio da microbiota intestinal é afetado na doença renal crônica (DRC), ocasionando o quadro de disbiose intestinal. Estes estudos sugeriram uma associação da disbiose intestinal com complicações metabólicas como acúmulo de toxinas urêmicas, progressão da DRC, inflamação e risco cardiovascular. Diante disso, medidas com o objetivo de restaurar o equilíbrio da microbiota intestinal são sugeridas, tais como a ingestão oral de probióticos, mas poucos estudos têm abordado o efeito destes suplementos na progressão da DRC e no risco cardiovascular destes pacientes. Objetivo: Avaliar o efeito do consumo de probióticos em fatores associados com progressão da DRC e risco cardiovascular de pacientes com DRC. Material e métodos: Trata-se de um estudo clínico controlado por placebo registrado no Clinical Trials NCT03400228. O estudo incluiu 30 pacientes adultos com DRC nos estágios 3 a 5 não em diálise, com função renal estável e proteinúria igual ou superior a 500 mg. A coleta de dados ocorreu entre novembro de 2015 até dezembro de 2017. O protocolo do estudo constou de período de washout de 4 semanas e randomização dos pacientes para o grupo de intervenção (GI, suplemento com probiótico) ou para o grupo controle (GC, maltodextrina). Foi realizado avaliação basal e após 24 semanas de consumo de probiótico ou placebo. Todos os pacientes receberam a orientação de consumir 2 sachês por dia do probiótico ou do placebo (maltodextrina). Foram avaliadas variáveis demográficas, clínicas, nutricionais, hábito intestinal e exames laboratoriais com amostras sanguíneas e urinárias. Resultados: Dos 30 pacientes incluídos, 20 completaram as 24 semanas do estudo, sendo 10 no grupo intervenção e 10 no grupo placebo. Após o uso de probiótico houve aumento na taxa de filtração glomerular estimada (p<0,001) e diminuição nos níveis séricos de creatinina (p<0,001), ureia (p=0,015), proteína C reativa (p=0,03), hormônio da paratireóide (p=0,03) e potássio (p=0,012), em comparação ao grupo placebo. Os efeitos positivos do probiótico na taxa de filtração glomerular estimada e na diminuição dos níveis séricos de creatinina e ureia permaneceram após análise de regressão multivariada. Não houveram diferenças significativas nos parâmetros urinários entre os grupos. Sintomas de constipação (p<0,001) e consistência fecal (p=0,016) apresentaram melhora no grupo intervenção versus placebo. Conclusão: A suplementação de probióticos melhorou os marcadores de função renal e reduziu inflamação, além de auxiliar na melhora dos sintomas de constipação intestinal em pacientes com DRC. / Introduction: The human gastrointestinal tract is colonized by a diversified microbial community that acts in control of health. Recent studies have shown that intestinal microbiota balance is affected in chronic kidney disease (CKD) leading to intestinal dysbiosis. These studies have suggested association of intestinal dysbiosis with several metabolic disorders such as accumulation of uremic toxins, progression of CKD, inflammation and cardiovascular risk. Therefore, interventional measurement that improve intestinal microbiota balance are suggested such as supplementation of probiotics, however few studies evaluated the effect of these supplements on the progression of CKD and cardiovascular risk in CKD patients. Aim: The purpose of the study was to evaluate the effects of probiotic supplementation on the factors associated with progression of CKD and cardiovascular risk in patients with CKD. Desing and Methods: This was a randomized, double-blind, placebo-controlled study. Thirty patients with CKD stages 3 to 5 not on dialysis, with stable renal function and protein-creatinine ratio > 0.50 were included. Data collection was between November 2015 and December 2017. Study protocol was 4-week washout period, patients randomized to intervention group (IG, probiotic supplement) or control group (CG, maltodextrin), and follow for 24 weeks. Renal function, C-reactive protein (CRP), bone and mineral metabolism, nutritional, and lipid profile markers and intestinal habit were measured at baseline and 24 weeks of study. Results: From 30 patients included in this study, 20 completed the 24 study weeks, 10 in the TG and 10 in PG. After probiotic supplementation, there was increase in estimated glomerular filtration rate (p<0.001) and decrease in serum creatinine 8 (p<0.001), urea (p=0.015), C-reactive protein (p=0.030), parathyroid hormone (p=0.03), and potassium (p=0.012) levels compared to CG. The beneficials effects of probiotics on estimated glomerular filtration rate and serum creatinine, urea, and Creactive protein remained after multivariate linear regression. There were no significant differences in the urinary parameters between the two groups. Symptoms of constipation (p<0.001) and stool consistency (p=0.016) improved in IG compared to CG. Conclusion: Probiotic supplementation improved markers of renal function and reduced inflammation. In addition, it improved the symptoms of intestinal constipation in patients with CKD.

Challenged by a huge and diverse antigenic stimulus, the intestinal mucosa has developed a unique immune system that mainly functions to maintain tolerance to innocuous antigens while retaining the ability to respond swiftly to pathogenic threats. Central to this specialised immune system are the Intraepithelial Lymphocytes (IELs). These cells are uniquely located between Intestinal Epithelial Cells (IECs) ready to respond to exogenous antigens in the intestinal lumen. The intestinal immune system is constantly influenced, not only by the commensal microbiota, but also by the nutritional status of the host and the availability of certain essential micronutrients that are derived from a healthy-balanced diet. Additionally, age has a significant impact on the efficiency of gut immunity in responding to infectious pathogens, as reflected by the increased burden of gastrointestinal infections at the extremes of age. In this thesis, using the Murine Norovirus (MNV) oral infection model, I aimed to characterize intestinal mucosal antiviral-responses with specific focus on the role of IELs, the impact of aging and the influence of certain micronutrients whose effects are mediated through the Aryl Hydrocarbon Receptor (AhR). Employing different knock-out and adoptive transfer experiments, I concluded that, at least in our experimental conditions and in a viral strain-specific manner, the activated IELs are not essential and may play a minor role in the protective response against MNV infection. This work also demonstrated that various MNV virus strains activate IELs differentially and for the first time (to our knowledge) revealed distinct abilities of these different Norovirus variants to infect IECs. Recognising an impaired response in old (2-year) mice, we were also able to identify a specific defect in the IFN-Lambda response of aged IECs. Furthermore, using the model of MNV infection to investigate the role of AhR signalling, the data I generated suggested a direct link between constitutive AhR signalling and innate interferon-mediated responses. These findings have uncovered a potential preventive/therapeutic targets for enhancing anti-viral responses.

Le microbiote digestif, composé de 1012 à 1014 bactéries par gramme de selle, est dominé par les bactéries anaérobies. Ces dernières, qui dépassent largement les aérobies, ont été découvertes en 1865 par Louis Pasteur dans ses travaux sur la fermentation. Les bactéries anaérobies représentent un intérêt médical particulier par leur implication dans les maladies infectieuses et métaboliques. Les anaérobies sont caractérisés par leur difficulté à être cultivés, car nécessitant une absence ou des concentrations faibles d’oxygène. Ainsi les connaissances sur ces microorganismes étaient limitées. Cependant, avec l’avènement des outils de biologie moléculaire notamment le séquençage à haut débit et le concept culturomics associé à l’identification par spectrométrie de mass MALDI-TOF, la connaissance des microorganismes anaérobies a été accentuée. Dans ce travail, nous nous sommes attelés dans un premier temps à la mise au point d’un milieu de culture efficace pour la culture des bactéries anaérobies et les tests d’activités antimicrobiennes. Nous avons montré dans un deuxième temps que culturomics, associé au MALDI-TOF, était un outil puissant dans l’identification des bactéries anaérobies en microbiologie clinique, mais également dans l’exploration de la diversité microbienne du tube digestif. Cette technique nous a permis d’isoler 19 nouvelles espèces de bactéries anaérobies dont 9 ont été décrites dans la troisième partie de ce travail. / The human gut microbiota is known to contain around 1012 to 1014 bacteria per gram of feces, with the majority being anaerobic. The latters were first discovered in 1865 by Louis Pasteur while working on fermentation. Anaerobic bacteria are known to play an important role in health and diseases and thus have taken a lot of attention in the medical field, especially in infectiousdiseases and metabolism. These bacteria are known for its sophisticated culture system because its growth requires little to no oxygen. Nevertheless, few is known about these type of microorganisms but with the advancement of molecular biology and sequencing techniques, its study became wider. Culturomics, is a recently developed culture-based approach that relies on optimizing culture conditions for bacterial growth and its identification by MALDI-TOF MS and 16S rRNA sequencing. The present work aims to create and optimized culture condition for anaerobic bacteria along with testing its anaerobic activities. Also, we aim to demonstrate the efficiency of Culturomics and MALDI-TOF in culturing, identifying and describing anaerobic bacteria in clinical microbiology and in the human gut. This approach allowed us to isolate 19 new anaerobic species out of which 9 has been described in this work.Keywords: Human gut microbiota, culture of anaerobic bacteria, culturomics, MALDI-TOF.

As limitações ao uso de antibióticos promotores de crescimento vêm aumentando a procura por aditivos substitutos para manter a performance animal, a saúde intestinal e a resposta imune de frangos de corte. Este experimento foi conduzido para comparar o efeito e a dose resposta do produto Ava Cid P (composto por substância húmica, butirato de sódio 30% protegido e uma pequena porção de acidificantes) suplementado na dieta, sobre a performance, resposta imune e saúde intestinal de frangos de corte. O experimento seguiu um design inteiramente casualizado, envolvendo um arranjo fatorial 2 x 5 (2 sexos e 5 tratamentos) com 7 repetições de 15 aves por tratamento. Os tratamentos seguiram a suplementação em diferentes fases de 1 a 49 dias: 1) Controle: dieta basal sem nenhuma suplementação; 2) AVA1-21: aves receberam 0,91 kg/t de Ava Cid P de 1 a 21 d; 3) AVA1-35: 0,91 kg/t de Ava Cid P de 1-21 d e 0,45 kg/t de 22-35 d; 4) AVA1-42: 0,91 kg/t de Ava Cid P de 1 a 21 d e 0,45 kg/t de 22- 42 d; 5) AVA1-49: 0,91 kg/t de Ava Cid P de 1 a 21 d, 0,45 kg/t de 22-35 d e 0,23 kg/t de 36-49 d. A suplementação com Ava Cid P não influenciou a performance de machos e fêmeas, nem mesmo a densidade de células caliciformes (P > 0,05). No entanto, o Ava Cid P foi capaz de modificar a morfometria intestinal, aumentando a altura de vilosidades aos 9 e 35 d (P < 0,05). A área superficial aparente dos vilos e altura de vilos, nas aves que receberam Ava Cid P durante todas as fases experimentais, foi superior à das aves suplementadas somente na fase inicial. No íleo, a área superficial aparente dos vilos também foi superior nas aves suplementadas aos 9 d. Além disso, a expressão do gene para mucina 2 (MUC2) e para o fator de necrose tumoral (TNF-α) diminuiu nas aves recebendo Ava Cid P aos 21 d (P < 0,05), mas não foram observadas diferenças estatísticas para interleucina-1 beta e interleucina-10. Os resultados sugerem que Ava Cid P pode alterar a expressão de mRNA de algumas citocinas e MUC2 e a morfometria intestinal de frangos de corte, aumentando a superfície aparente e a altura dos vilos, o que demonstra a potencialidade do produto como alternativa aos antibióticos promotores de crescimento. / The limitations of the antibiotic growth promoter’s (AGP) usage have been increasing the search for new products to improve poultry performance, gut healthy and immune response. This experiment was conducted to compare the effect and dose response of Ava Cid P (consisted of a humic substance, coated sodium butyrate 30% and a small acidifier portion) diet supplementation on performance, immune response and gut health of broilers. Five dietary regimens were used: 1) birds didn’t receive Ava Cid P in any phase (Control), 2) birds received 0.91 kg/t of Ava Cid P from 1 to 21 d (AVA1-21), 3) 0.91 kg/t of Ava Cid P from 1 to 21 d and 0.45 kg/t from 22 to 35 d (AVA1-35), 4) 0.91 kg/t of Ava Cid P from 1 to 21 d and 0.45 kg/t from 22 to 42 d (AVA1-42), 5) 0.91 kg/t of Ava Cid P from 1 to 21 d, 0.45 kg/t from 22 to 35 d and 0.23 kg/t from 36 to 49 d (AVA1-49). They were applied in a completely randomized design, involving a 2 × 5 factorial arrangement with 2 sex and 5 levels of inclusion, and 7 replications with 15 birds each. The supplementation with Ava Cid P showed no influence on males and females growth performance and goblet cell density (P > 0.05). However, it modified the gut morphometry, increasing jejunum villi height at 9 and 35 days (P < 0.05). The apparent villus surface area and villi height on birds fed with Ava Cid P during all phases also increased in relation to those who received only in the early phase. The expression of mucin 2 (MUC2) and tumor necrosis factor-alpha (TNF-α) decreased on birds that received Ava Cid P at 21 days (P < 0.05), but no differences were seen for interleukin-1beta (IL-1β) and interleukin-10 (IL-10). The results suggest that Ava Cid P can alter the mRNA expression of some inter-leukins, MUC2 and intestinal morphometry in broilers, increasing apparent villus surface area and villi height, which demonstrates the product potential as an alternative growth promoter.