Dissertations / Theses: 'Microbiome bactérien'

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Nguyen, Do Ngoc Linh. "Mise au point de l’analyse par séquençage à haut-débit du microbiote fongique et bactérien respiratoire chez les patients atteints de mucoviscidose." Thesis, Lille 2, 2016. http://www.theses.fr/2016LIL2S011/document.

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L’infection broncho-pulmonaire représente le problème majeur des malades atteints de la mucoviscidose. Plusieurs bactéries sont connues depuis des dizaines années comme les principaux agents responsables de ces infections (par exemple Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia cepacia, Achromobacter xylosoxidans…). Récemment, certains genres fongiques notamment les champignons filamenteux (comme Aspergillus, Scedosporium…) ont été identifiés comme des pathogènes émergeants ou ré-émergeants pouvant être responsables d’infection invasive. Ainsi, la détection des microorganismes impliqués dans ces colonisations et/ou infections respiratoires demeure importante sur le plan physiopathologique et clinique.Si la culture microbiologique reste la méthode la plus utilisée à ce jour pour le diagnostic des infections microbiennes, elle ne permet pas d’identifier les microbes non-cultivables ou difficiles à cultiver. Depuis quelques années, grâce au développement de la technique moléculaire de séquençage à haut-débit (next generation sequencing ou NGS), plusieurs études ont montré que l’écologie microbienne du poumon des patients atteints de la mucoviscidose est très complexe et correspond à une flore poly-microbienne, appelée le microbiote pulmonaire, comprenant non seulement des bactéries mais également des micromycètes (levures et/ou champignons filamenteux) et des virus et phages. Une dysbiose (modification en abondance et diversité) de cette flore pourrait influencer la fonction respiratoire et l’état clinique du patient.Alors que le microbiome bactérien et son rôle en pathogenèse sont largement étudiés, peu d’études ont porté sur la composante fongique (mycobiote/mycobiome) du microbiote pulmonaire. Notre travail de thèse s’inscrit dans les différents projets développés au sein de l’axe de recherche « Microbiote pro- et eucaryote pulmonaire » coordonné par le Pr Laurence Delhaes dans l’équipe Biologie et Diversité des Pathogènes Eucaryotes Emergeants (BDPEE) dirigée par le Dr Eric Viscogliosi. Il se focalise sur l’analyse NGS du microbiote pro- et eucaryotique respiratoire chez les patients atteints de la mucoviscidose et notamment la comparaison de différentes approches méthodologiques en vue d’une optimisation et standardisation de la méthode.Dans un premier temps, nous présenterons une synthèse des connaissances actuelles d’une part des phénomènes de colonisations/infections fongiques chez les patients atteints de mucoviscidose et d’autre part dans le domaine du microbiote pulmonaire et surtout du mycobiote pulmonaire autour duquel notre équipe se focalise.2Dans un deuxième temps, nous avons travaillé à mieux adapter l’approche NGS aux études du microbiote pulmonaire dans la mucoviscidose. En effet, le séquençage à haut-débit est une technique puissante mais pour laquelle des biais peuvent être introduits à de nombreuses étapes méthodologiques. Un des biais les plus importants est que l’approche NGS ne permet pas de différencier les microorganismes vivants, des cellules mortes ou endommagées, ni de l’ADN extracellulaire. Dans le contexte de notre travail –celui du microbiote pulmonaire chez des patients atteints de mucoviscidose et souvent exposés aux antibiotiques par voie intraveineuse à forte dose, l’analyse NGS pourrait évaluer incorrectement l’abondance et la diversité de ce microbiote pulmonaire. Un prétraitement des échantillons par propidium monoazide (PMA), qui permet de cibler sélectivement l’ADN des cellules vivantes, pourrait être une solution pour palier à cette limite. Notre étude avait donc comme objectif de déterminer si un prétraitement par PMA des expectorations modifiait le microbiote pro- et eucaryote pulmonaire analysé par NGS. Nous discutons l’intérêt et la relevance clinique de cette approche « PMA - NGS » permettant une quantification isolée des microorganismes vivants dans le contexte de la mucoviscidose
Chronic pulmonary infection results in an irreversible decline in lung function in patients with cystic fibrosis (CF). While several bacteria are known as main causes for these infections (for example: Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia cepacia, Achromobacter xylosoxidans...), more recently some fungal genera including filamentous fungi (such as Aspergillus, Scedosporium...) have also been identified as emerging or re-emerging pathogens able to cause invasive mycosis. Thus, the identification of the microorganisms involved in the respiratory colonizations and/or infections has become essential.Still now culture methods remain the gold standard for diagnostic of microbial infections. However, it could not identify non-culturable or difficult-to-cultivate microorganisms. Thanks to the development of high-throughput sequencing (next generation sequencing or NGS), recent studies have shown that the lung of patients with CF is a complex poly-microbial flora, also called the CF lung microbiota, which includes not only bacteria but also fungi (yeast and/or filamentous fungi), and viruses and phages. Dysbiosis (loss of abundance and/or diversity) of the lung microbiota has been associated with the patient's decreased lung function and poor clinical status.While lung bacteriota and its role in pathogenesis have widely been studied, few research studies focus on the fungal component (mycobiota/ mycobiome) of the lungs. Our thesis (PhD work) focuses on NGS analysis of pro- and eukaryotic lung microbiota in CF patients, in particular on the comparison of different methodological approaches to optimize and standardize the NGS protocol. This project has been developed under the supervision of Pr. Laurence Delhaes in the “Biology and Diversity of Eukaryotic Emerging Pathogens” team directed by Dr. Eric Viscogliosi.Firstly, we present a state of art on the current knowledge on the fungal colonization/infections risk in CF as well as the development of new concepts of lung microbiota and lung mycobiota on which our team focuses.Secondly, we applied the NGS approach to study the pro- and eukaryotic microbiota in the sputum samples of CF patient lung. Indeed, NGS is a powerful technique that may introduce biases on numerous methodological steps. One of the most important biases is that this technique could not differentiate among the living microorganisms, the dead or damaged cells, and the extracellular DNA. In the context of the CF lung microbiota which is often exposed to high-dose intravenous antibiotics, the analysis by NGS might evaluate4inaccurately the abundance and the diversity of the lung microbiota. Pretreatment of samples by propidium monoazide (PMA), which can target selectively the DNA of viable cells, could be a solution to overcome this limitation. Our study aimed to determine whether a sample pretreatment with PMA modified the lung pro- and eukaryotic microbiota analyzed by NGS. We discuss the clinical relevance of this approach "PMA - NGS" in the context of CF patients to a better quantification of living microorganisms

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Sharma, Poonam. "Genome analysis of multidrug resistant bacteria from patients with cystic fibrosis." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5096.

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La mucoviscidose est une maladie génétique autosomique causée par une mutation dans le gène CFTR (Cystic Fibrosis Transmembrane Conductance Regulator). Mon travail s’est décomposé en deux parties principales : d’une part j’ai réalisé une revue de la littérature sur l’analyse des génomes bactériens isolés de patients mucoviscidosiques comparativement aux génomes des mêmes espèces isolées dans d’autrescontextes et d’autre part j’ai analysé les génomes de trois espèces bactériennes (Microbacterium yannicii, Chryseobacterium oranimense et Haemophilus parahaemolyticus). L’analyse exhaustive des génomes bactériens issus de patients atteints de mucoviscidose a révélé une extraordinaire évolution de ces génomes en fonction du temps et des traitements reçus par ces patients qui témoigne de la capacité qu’ont ces bactéries à s’adapter à leur écosystème notamment par l’acquisition de nouveaux gènes par transfert latéral de gènes. Ce travail montre l’extraordinaire plasticité des génomes bactériens dans un milieu donné et à ce titre le poumon de patients atteints de mucoviscidose représente un modèle unique pour comprendre l’évolution des génomes bactériens. De plus, notre travail a permis d’identifier leurs mécanismes moléculaires de résistance aux antibiotiques. Les travaux à venir sur l’étude des métagénomes de prélèvements chez ces patients pourrait permettre de répondre à ces questions dans le futur. La découverte de nouvelles espèces et / ou émergentes va nous permettre d’avoir une image plus complète de la mucoviscidose qui pourrait conduire à une meilleure connaissance de la maladie et donc à une meilleure prise en charge thérapeutique
Cystic fibrosis is an autosomal genetic disorder caused by a mutation in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene. Pulmonary infection is the major problem faced by patients with cystic fibrosis. My work is divided into two main parts: first I made a review of the literature on the analysis of bacterial genomes isolated from CF patients compared to the genomes of the same species isolated in autrescontextes and other part I analyzed the genomes of three species of bacteria (Microbacterium yannicii, Chryseobacterium oranimense and Haemophilus parahaemolyticus). The comprehensive analysis of bacterial genomes from cystic fibrosis patients revealed an extraordinary evolution of these genomes with time and treatment received by these patients reflects the ability of these bacteria to adapt to their particular ecosystem the acquisition of new genes by lateral gene transfer. This work shows the extraordinary plasticity of bacterial genomes in a given environment and as the lungs of patients with cystic fibrosis represents a unique model for understanding the evolution of bacterial genomes. In addition, our work has identified their molecular mechanisms of resistance to antibiotics. Future work on the study of metagenomes sampling in these patients could help to answer these questions in the future. The discovery of new species and / or emerging will allow us to have a more complete picture of cystic fibrosis which could lead to a better understanding of the disease and thus a better therapeutic management

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Durand, Guillaume. "Incompatibilités de culture bactérienne." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0705/document.

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L’étude du microbiote digestif est un enjeu important de recherche en microbiologie. La première partie de cette thèse porte sur la recherche au sein du microbiote digestif de nouveaux antibactériens, qui apparait comme une des pistes clés dans la lutte contre la résistance aux antibiotiques. Les trois quarts des antibiotiques sont des produits naturels, ou dérivés, sécrétés par des microorganismes de l’environnement. Comme lui, le microbiote digestif représente un écosystème complexe où règne une grande compétition. Nous avons recherché des antagonismes de culture dans le microbiote digestif contre les bactéries les plus pathogènes pour l’homme. Nous avons trouvé une inhibition de S. aureus par P. avidum, de E. cloacae par B. fragilis, E. dispar, L. delbruckii, P. acidipropionici, S. equinus, S. gallolyticus, et enfin de E. aerogenes par B. vulgatus et E. dispar. Nous avons également trouvé des clusters de gène de métabolites secondaires dans le génome de ces bactéries. Ce travail préliminaire confirme que le microbiote digestif est une source potentielle de nouveau antibactériens. En dépit de l’explosion du nombre d’espèces isolées dans le microbiote digestif grâce à la culturomics, certaines restent fastidieuses à cultiver. Nous avons analysé par métagénomique et culturomics une selle avant et après incubation anaérobie en présence de 5% de rumen et 5% de sang de mouton. Ce travail montre une dynamique de croissance des bactéries très hétérogène. Le milieu d’enrichissement utilisé était efficace et permettait la culture d’un plus grand nombre d’espèces bactériennes. Ce travail apporte des éléments nouveaux permettant l’optimisation de cette étape de culturomics
Gut microbiota is a major health concern for microbiologists. Its alterations were previously related to diseases. In the first step of this thesis, we have searched for new antimicrobials within the gut microbiota. Indeed, antibiotic resistance is a global health concern and research for new antibiotics is a cornerstone for fight against it, according to the WHO. Three quarter of all current antibiotics are natural products, or derived from them, synthesised by bacteria and fungi from soil. Gut microbiota is another complex ecosystem with strong competition. We have searched for antagonism in the gut microbiota species against most human pathogenic species. We found an inhibition of growth of S. aureus by P. avidum, of E.cloacae by B. fragilis, E. dispar, L. delbruckii, P. acidipropionici, S. equinus, S. gallolyticus,and an inhibition of E. aerogenes by B. vulgatus and E. dispar. We also found BGCs for all these species. This preliminary work confirm that gut microbiota is a potential source for new antibiotics. Despite the explosion of bacterial species isolated from gut, some fastidious species remains difficult to grow. We performed a metagenomic and culturomics analysis of a fresh stool sample before and after incubation into an anaerobic blood bottle supplemented with sheep blood and rumen fluid. This medium used in culturomics for enrichment was effective, allowing the isolation of higher number of species. This work show that the dynamic growth of bacteria is very variable. This work brings some precisions in the dynamic of bacterial growth that could improve the culturomics process

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Tidjani, Alou Maryam. "Etude du microbiote digestif des enfants atteints de malnutrition sévère aiguë." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5036/document.

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Depuis plusieurs années, il s’avère de plus en plus clair que le microbiote digestif a un impact remarquable sur la santé humaine. Il est affecté par de nombreux facteurs dont l’alimentation. En effet, en fonction du macronutriment majoritaire d’un régime alimentaire, certaines populations et fonctions bactériennes sont stimulées ou inhibées. Plusieurs pathologies de l’intestin ou liées à des troubles nutritionnels ou métaboliques ont un lien causal avec une altération du microbiote digestif parmi lesquelles la malnutrition sévère aigue. En effet, il a été récemment montré que le microbiote digestif des enfants malnutris était différent et colonisé par des Proteobacteria, des Enterococci, des bacilles Gram-négatifs et des espèces pathogènes. Au cours de nos travaux, une dysbiose est également observée chez nos patients malnutris par métagénomique et par culturomics avec un enrichissement en bactéries aérobies, en Proteobacteria et en espèces potentiellement pathogènes telles que Streptococcus gallolyticus et une perte notable en bactéries anaérobies associée à une perte de la capacité antioxydante du tractus gastro-intestinal révélée par une absence totale de Methanobrevibacter smitii, archeae méthanogène et un des procaryotes les plus sensibles à l’oxygène du tractus gastro-intestinal ainsi que un potentiel redox fécal accru. De plus, une perte de la diversité globale, connue et inconnue, est observée. Enfin, par culturomics et métagénomique, nous avons établi un répertoire des bactéries manquantes chez les malnutris dont treize présentent un potentiel probiotique et pourront être testées comme probiotiques dans un modèle expérimental dans un futur proche
For the last decade, it has become increasingly clear that the gut microbiota has a tremendous impact on human health. It is affected by several factors among which diet that has a big impact. In fact, according to the major macronutrient in a diet type, specific bacterial populations and functions are stimulated or inhibited. Several pathologies of the gut or linked to nutritional or metabolic disorders among which severe acute malnutrition are causally linked to an alteration of the diversity of the human gut microbiota. In fact, it has recently been shown by several studies that the gut microbiota of malnourished patients was different and colonized by Proteobacteria, Enterococci, Gram-negative bacilli and pathogenic species. The analysis of our data regarding the fecal microbiota of children afflicted with severe acute malnutrition from Niger and Senegal showed a dysbiosis observed through metagenomics and culturomics with an increase of aerobic bacteria, Proteobacteria and pathogenic species such as Streptococcus gallolyticus, and a depletion of anaerobic species associated with a loss of the antioxidant capacity of the gastro-intestinal tract exhibited by a total absence of Methanobrevibacter smithii, a methanogenic archaeon and one the most oxygen sensitive prokaryote of the gut microbiota alongside an increased fecal redox potential. Moreover, a loss of the overall diversity, known and unknown, was observed. Finally, through culturomics and metagenomics, we were able to identify a repertoire of missing microbes in malnourished children among which thirteen presented a probiotic potential and will be tested as such in an experimental model in the near future

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Bilen, Melhem. "Description of the human gut microbiota by culturomics." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0177/document.

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Le microbiote intestinal humain a été fortement corrélé avec la santé humaine et les maladies et a montré un potentiel dans les développements thérapeutiques. La métagénomique a déjà montré qu'elle était capable de générer beaucoup de données, dont certaines sont dénuées de sens et constituaient la "matière noire". Alors culturomics a été développée pour compléter la métagénomique en ciblant des espèces bactériennes précédemment non cultivées. En utilisant la culturomics, nous avons décrit le microbiote intestinal humain des Pygmées et réussi à isoler un nombre significatif d'espèces bactériennes parmi lesquelles 38 étaient de nouvelles espèces. En comparant les résultats métagénomiques aux données culturomics, on constate que seulement 26% des espèces isolées ont été récupérées par métagénomique et que jusqu'à 59% des Operational taxonomic units détectées correspondaient à de nouvelles espèces bactériennes isolées par culturomique dans cette étude ou dans les précédentes
The human gut microbiota has been correlated in general health and diseases. Thus its description became mandatory to better understand its role and therapeutic potential. However, metagenomics has previously showed to be able to generate a lot of data, of which some are meaningless and constituted the “Dark matter”. Thus, culturomics was developed to complement metagenomics by targeting previously uncultured bacterial species. Using culturomics, we described the human gut microbiota of Pygmy people and succeeded in isolating a significant number of bacterial species out of which 38 were new species. Comparing metagenomics results to culturomics data, we see that only 26% of the isolated species were recovered by metagenomics and that up to 59% of the Operational taxonomic units detected corresponded to new bacterial species isolated by culturomics either in this study or in previous ones

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Diop, Khoudia. "Caractérisation du microbiote des flores vaginales normales et de vaginose bactérienne." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0674/document.

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Grâce aux avancées de la technologie et nouvelles stratégies OMICS, de nombreuses études se sont intéressées au microbiote vaginal ces dernières années. Elles ont révélé l'impact de ce dernier sur la santé de la femme. En effet, un déséquilibre de la flore vaginale la rend vulnérable, la prédisposant à la vaginose bactérienne ainsi qu’à des complications gynéco-obstétricales sévères. La pathogénèse de la vaginose reste encore méconnue et le traitement classique par antibiothérapie échoue dans plus de 50% des cas. En analysant 50 prélèvements vaginaux provenant de patientes atteintes de vaginose et de femmes saines vivant en France et au Sénégal, nous avons constaté une plus grande diversité bactérienne chez les patientes par rapport aux témoins avec l'augmentation d'espèces telles que Gardnerella vaginalis, Atopobium vaginae ainsi que les procaryotes sensibles à l'oxygène, y compris les Cocci anaérobies à Gram-positif et les Prevotella. Les femmes saines renfermaient plus d’espèces de Lactobacillaceae et de Proteobacteria dans leurs flores. La combinaison de la métagénomique et la culturomique a permis d’identifier un complexe de 11 espèces/genres bactériens associés à la vaginose. L’utilisation de la culturomique a permis d’accroître le répertoire des bactéries humaines avec l’isolement de 27 nouvelles espèces. Le faible taux de recouvrement entre les données de métagénomique et celles de culturomique montre la nécessité de persévérer dans l’isolement des bactéries par culturomique. L’obtention d'isolats permettra d'explorer in vitro les compétitions entre les bactéries et pourrait servir également de matière première pour développer un traitement par bactériothérapie
Over the last decades, thanks to the technologic progresses including advanced molecular techniques and new OMICS strategies, many studies have focused on the vaginal microbiota. Thus, revealing the impact of the vaginal flora on women health. Indeed, the disruption of the vaginal bacterial community makes it prone to bacterial vaginosis and severe obstetrical and gynecological disorders. The pathogenesis of bacterial vaginosis is still unknown, and relapses are very frequent. Conventional treatment with antibiotic therapy fails in more than 50% of cases. The analysis of 50 vaginal samples from bacterial vaginosis patients and healthy women living in France and Senegal, showed a higher bacterial diversity in patients compared to controls with the increase of species such as Gardnerella vaginalis, Atopobium vaginae as well as oxygen-sensitive prokaryotes including Gram-positive anaerobic cocci, and Prevotella spp. Healthy women harbored more Lactobacillaceae species and Proteobacteria in their microbiota. The combination of metagenomics and culturomics has allowed the identification of a complex of 11 bacterial species/genera associated with bacterial vaginosis. The use of the culturomics approach has extended the repertoire of human-associated bacteria, with the isolation of 27 new bacterial species. The low range overlap between metagenomic and culturomics data indicates the need to continue the isolation of bacteria by culturomics. Obtaining isolates will make it possible to explore in vitro the competitions between the bacteria but can also be used as primary material for the development new treatments by bacteriotherapy

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Dione, Niokhor. "Exploration du microbiote digestif : stratégies de culture des bactéries anaérobies et de culture difficile." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0614.

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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

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Villain, Adrien. "Étude génomique des interactions diatomées-bactéries." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0202/document.

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Les diatomées sont des algues microscopiques qui contribuent à hauteur de 25% environ à la production primaire planétaire. Les diatomées sont très souvent entourées d’une flore bactérienne, avec laquelle de nombreuses interactions ont été documentées. Les génomes de diatomées contiennent par ailleurs de nombreux gènes dont l’origine prédite est bactérienne.Nous avons étudié Asterionella formosa, une diatomée pennée présente dans de nombreux lacs et cours d’eau à l'aide de données omiques. L’utilisation de la métagénomique a permis de reconstruire 30 génomes bactériens, utilisés pour prédire d'éventuelles interactions avec la diatomée. Le séquençage de la sous-unité 16S de l’ARN ribosomique a montré que les différentes espèces bactériennes avaient une abondance variable au cours des phases de croissance de la diatomée, et que certaines étaient plus souvent au contact de la diatomée que libres dans le milieu. Le génome d'A. formosa a ensuite été séquencé à l'aide de la technologie Pacbio et comparé à ceux d'espèces proches. Enfin, l’impact des bactéries sur les diatomées a été abordé sous l’angle de l’évolution et des transferts horizontaux de gènes, qui ont été prédits à partir des données transcriptomiques d’une centaine de diatomées marines.Ce travail représente une première étape dans l'étude de la communauté bactérienne associée à A. formosa. Des expériences complémentaires incluant l’utilisation de transcriptomique ou métabolomique sont maintenant envisageables. Les données collectées et/ou analysées dans ce travail contribuent d'ores et déjà à l’effort global de caractérisation génomique des diatomées
Diatoms are ubiquitous microalgae that contribute approximately 25% to the primary production worldwide. Many interactions, either positive, neutral or negative, have been documented between diatoms and bacteria. Diatom genomes also harbor numerous genes of putative bacterial origin.We are studying Asterionella formosa, a freshwater pennate diatom. We characterized the community using a combination of omics and laboratory techniques. We reconstructed of the genome of the diatom as well as 30 individual genomes from co-cultured bacterial species and investigated metabolisms that could support diatom-bacteria interactions. 16S rRNA sequencing revealed that the abundance of some bacterial species was highly variable over the course of A. formosa growth. Some species seemed preferentially attached to the diatom while others were mainly free-living. Then, the reference sequence of the A. formosa genome was improved by additional long-read (Pacbio) sequencing. Last, relationships between diatoms and bacteria were investigated at a broader evolutionary scale, by looking at horizontal gene transfers using transcriptomic data of a hundred marine diatoms.This work is a first step in the study of the dynamic and complex bacterial community associated with the diatom A. formosa. The accurate identification and the reconstruction of the genome of these bacteria will enable further in silico predictions based on metabolic networks and new omics experiments using transcriptomic or metabolomic. This work already contributes to a global effort to study diatoms by the means of genomics

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Bellone, Rachel. "Aspects moléculaires de l'influence de la température sur la transmission du virus du chikungunya par le moustique Aedes albopictus." Electronic Thesis or Diss., Sorbonne université, 2021. http://www.theses.fr/2021SORUS072.

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Le virus du chikungunya (CHIKV) est un arbovirus émergeant qui, au cours des dernières décennies, s’est largement propagé à l’échelle mondiale. Le virus est transmis par les moustiques du genre Aedes, notamment Aedes albopictus qui est aujourd’hui présent dans une soixantaine de départements en France. Vecteurs de plusieurs agents pathogènes, Ae. albopictus représente une réelle menace de santé publique. L’émergence d’arboviroses est généralement liée à la convergence d’un ensemble de facteurs intrinsèques et extrinsèques affectant le vecteur, l’agent pathogène et l’hôte. Le moustique étant un organisme ectotherme, dont la température interne varie avec celle de l’environnement, il est très sensible aux variations de température du milieu ambiant. La relation entre la température et la transmission des arbovirus reste encore mal comprise, en particulier sur le plan moléculaire. L’objectif général de ce projet est de comprendre comment la température affecte les interactions virus-moustique et influence les cycles de transmission. Pour cela, nous étudions les aspects moléculaires du CHIKV, de son vecteur Ae. albopictus et de leurs interactions sous l’influence de la température. Nos résultats démontrent que la température affecte d’une part l’évolution du CHIKV et d’autre part, l’expression génétique et la composition microbienne du moustique, notamment en réponse à l’infection. Ces données apportent des informations importantes sur la manière dont les systèmes vectoriels peuvent être affectés par la température. La compréhension des mécanismes sous-jacents les interactions virus-moustique avec l’environnement sont essentielles afin de prévenir les épidémies
The chikungunya virus (CHIKV) is an emerging mosquito-borne Alphavirus which has widely spread around the world in the last two decades. The virus is transmitted to human hosts by Aedes mosquitoes, including the invasive species Aedes albopictus, which has today conquered more than half of the French territory. As a vector of several viral pathogens, Ae. albopictus poses a real threat to the health authorities. The emergence of arboviruses such as CHIKV, often results from a complex combination of both intrinsic and extrinsic factors. Since mosquitoes are poikilothermic ectotherms (i.e., internal body temperature is not constant and depends on environmental temperatures), they are acutely susceptible to temperature variations. The relation between temperature and arbovirus transmission is a complex phenomenon that remains poorly understood, especially at the molecular level. The aim of our project is to better understand how temperature affects mosquito-virus interactions and influences transmission cycles. We study the molecular aspects of CHIKV, its vector Ae. albopictus and their interactions under the influence of temperature. Our results show that temperature affects CHIKV evolution as well as mosquito genetic expression and microbial composition, especially in response to infection. These data provide important information on how vector systems can be affected by temperature. Understanding the mechanisms underlying virus-mosquito interactions with the environment is essential in order to prevent epidemics

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Traore, Sory Ibrahima. "Etude de microbiote digestif africain par culturomics et nouvelle technique d'isolement et de culture de Methanobrevibacter smithii." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0672/document.

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L’étude du microbiote digestif a connu un regain d’intérêt au début des années 2000, avec l’avènement des techniques moléculaires. La culturomics a démontré sa complémentarité depuis 2010 en réduisant une partie des biais des méthodes moléculaires. Une revue sur les techniques d’étude du microbiote digestif et l’analyse du microbiote des sujets africains. Les études de métagénomique en Afrique ont révélé une augmentation de la biodiversité, en particulier des Spirochaetes et des Prevotella chez les africains par rapport aux occidentaux. Sur les 1162 bactéries isolées par culturomics, 476 n'étaient pas africaines, 445 étaient communes et 241 étaient d’origine africaine dont 68 nouvelles espèces. Pour ma participation au travail de culturomics, 102750 colonies testées par MALDI-TOF,ont permis d'identifier 377 espèces incluant 40 nouvelles espèces,17 nouveaux genres et 2 nouvelles familles.Ces nouvelles espèces ont été décrites par taxonogenomics ou new species announcement.Les archaea méthanogènes ont une prévalence de 97,4% pour M. smithii et associés à des pathologies comme l’abcès du cerveau,les parodontites etc. La culture est fastidieuse et nécessitait une source extérieure d’hydrogène. Sous enceinte anaérobie, nous avons cultivé avec succès M. smithii à partir d’un milieu de culture liquide inoculé d’échantillon de selle. L’isolement en culture pure a été un succès sur milieu gélosé en réalisant une coculture avec Bacteroides thetaiotaomicron. Nous avons aussi testé avec succès la coculture de M. smithii avec d’autres bactéries productrices d’hydrogène connues. Les tests de chromatographie en phase gazeuse montraient que ces souches produisaient de l’hydrogène
The study of the digestive microbiota was a renewed interest in the early 2000s, with the advent of molecular techniques. The culturomics has demonstrated its complementarity since 2010 by reducing some of the biases of molecular methods. A review on the techniques of studying the digestive microbiota and the analysis of the microbiota of African subjects. Metagenomic studies in Africa have revealed an increase in biodiversity, especially Spirochaetes and Prevotella among Africans compared to Westerners. Of the 1162 bacteria isolated by culturomics, 476 were non-African, 445 were common, and 241 were of African origin, including 68 new species. For my participation in the work of culturomics, 102750 colonies tested by MALDI-TOF, identified 377 species including 40 new species, 17 new genera and 2 new families. These new species have been described by taxonogenomics or new species announcement.Methanogenic archaea have a prevalence of 97.4% for M. smithii and associated with pathologies such as brain abscess, periodontitis and so on. The cultivation is tedious and required an external source of hydrogen. Under anaerobic enclosure, we successfully cultivated M. smithii from a liquid culture medium inoculated with a stool sample. The isolation in pure culture was a success on agar medium by performing a coculture with Bacteroides thetaiotaomicron. We have also successfully tested the co-culture of M. smithii with other known hydrogen-producing bacteria. Gas chromatographic tests showed that these strains produced hydrogen

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Ndongo, Sokhna. "Culture et description des bactéries anaérobies strictes du microbiote digestif." Thesis, Aix-Marseille, 2019. http://www.theses.fr/2019AIXM0627.

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Le microbiote intestinal est largement dominé par les bactéries anaérobies strictes et de nombreux efforts ont été consacrés à l'isolement de ses microorganismes. Cependant, ces efforts restent insuffisants par rapport à leur implication croissante dans les infections et pathologies humaines. L’isolement des bactéries anaérobies strictes reste un processus difficile, fastidieux et à faible débit dû probablement à des obstacles tels que le manque d’informations sur leur biologie et leur écologie. En utilisant le concept de Microbial culturomics dans cette thèse, nous avons mis en place des stratégies et techniques de culture pour optimiser l’isolement des bactéries intolérantes à l’oxygène mais aussi des espèces d’intérêt médical majeur. Dans un premier temps, 200 échantillons de selles fraiches provenant du laboratoire de routine de l’hôpital de la Timone (France, Marseille) ont été analysés. Nous avons isolé 60 nouvelles espèces bactériennes dont 54 étaient des bactéries anaérobies strictes et 1 appartenant au phylum des Synergistes (phylum très rare). Ensuite nous avons pu isoler à partir de selles fraiches provenant de 9 donneurs volontaires sains, 12 nouvelles souches d’une espèce nommée Faecalibacterium massiliensis et une autre nouvelle espèce nommée Faecalibacterium timonensis. Plusieurs souches d’Akkermansia muciniphila ont été isolées au cours de ce travail. De plus, nous avons également réussi à isoler deux nouvelles espèces de Christensenella (C. massiliensis et C. timonensis). Grâce à l’approche Taxonogénomique, plusieurs espèces ont été décrites et la diversité des espèces du genre Faecalibacterium a été mise en évidence pour la première fois
Intestinal microbiota was largely dominated by strict anaerobic bacteria, and many efforts have been devoted to isolate of these microorganisms. However, these efforts remain insufficient to report their increasing involvement in human infections and diseases. The isolation of strict anaerobic bacteria remains difficult, fastidious and at low throughput, probably due to obstacles such as a lack of information on their biology and ecology. Using Microbial Culturomics concept in this thesis, we have implemented strategies and culture techniques to optimize the isolation of oxygen-intolerant bacteria as well as species of major medical interest. In the first time, 200 fresh stool samples from the routine laboratory from Timone Hospital (France, Marseille) were analysed. We isolated 60 new bacterial species of which, 54 were strict anaerobic bacteria and one belonged to the Synergists phylum (very rare phylum). Thus, we were able to isolate 12 new strains of a species called Faecalibacterium massiliensis and another new species called Faecalibacterium timonensis from fresh stools of healthy volunteer donors. Several strains of Akkermansia muciniphila have been isolated during this work. In addition, we were also able to isolate two new species of Christensenella (C.massiliensis and C. timonensis). Through the Taxonogenomic approach, several species have been described and the diversity of species of the genus Faecalibacterium has been highlighted for the first time

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Perrin, Yoann. "Étude des communautés bactériennes d’un réseau d’eau potable. Influence des paramètres environnementaux." Thesis, Poitiers, 2018. http://www.theses.fr/2018POIT2289/document.

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Les bactéries sont une composante indissociable des réseaux de distribution d’eau potable qui, en les colonisant, forment des communautés complexes. Il est émis l’hypothèse que des variations de structure et de composition de ce microbiome pourraient refléter des changements de la qualité de l’eau liés à différents phénomènes (stagnation, biocorrosion, changement de pression, ...). Une importante campagne de prélèvements menée sur le réseau d’eau potable de Paris a permis d’apprécier la dynamique de ces communautés bactériennes selon trois méthodes différentes : la description de la communauté par metabarcoding, la culture de la flore hétérotrophe totale et la quantification par PCR de trois pathogènes opportunistes, Mycobacterium spp. L. pneumophila, et P. aeruginosa. Cette étude a mis en évidence une certaine diversité au sein des communautés bactériennes de l’eau potable malgré une prédominance des genres Hyphomicrobium et Phreatobacter. Les méthodes de culture et de PCR quantitative mettent également à jour l’importance écologique du genre Mycobacterium. L’intégration aux analyses des paramètres spatio-temporels et physico-chimiques de l’eau potable a permis de constater une relative stabilité des communautés bactériennes. Cependant, suite à d’importants évènements climatiques, des variations dans la structure des communautés sont visibles sans conséquence sur la qualité sanitaire de l’eau. Ces travaux suggèrent que l’utilisation en parallèle de différentes méthodologies, et notamment l’apport du metabarcoding, permet d’améliorer la connaissance sur le réseau de distribution d’eau potable et de mieux observer des changements fins, invisibles aux méthodes classiques
Bacteria are an indivisible component of drinking water distribution systems which, by colonizing them, form complex communities. It is assumed that variations in the structure and composition of this microbiome could reflect a change in water quality related to different events (stagnation, biocorrosion, pressure change, etc.). A major sampling campaign was conducted within the Paris drinking water distribution systems allowing to assess the diversity and the dynamic of these bacterial communities using three different methods: description of the community by metabarcoding, heterotrophic plate count and quantification by PCR of three opportunistic pathogens, Mycobacterium spp. L. pneumophila, and P. aeruginosa. This study revealed some diversity within the drinking water bacterial communities. Culture and quantitative PCR methods also reveal the ecological importance of the Mycobacterium genus. The integration of spatio-temporal and physico-chemical parameters of drinking water into analyses has highlighted a relative stability of bacterial communities. However, variations in the structure of the communities are visible following important climatic events, without consequences on the sanitary quality of the water. Altogether, our work suggests that the use in parallel of different methodologies, particularly metabarcoding, has improved our knowledge of the bacterial communities within the Paris drinking water distribution systems and better observe subtle changes, invisible to conventional methods

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Guilhot, Elodie. "Techniques de culture pour l'étude du microbiote digestif anaérobie." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0611.

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Les microorganismes anaérobies représentent la population majoritaire de notre tube digestif et ont un impact remarquable sur notre santé. Leur culture demeure à ce jour longue, fastidieuse et coûteuse et nombreux sont ceux qui restent incultivables. Or la culture est un outil indispensable pour l'étude du microbiote digestif. Ainsi, le laboratoire dans lequel ma thèse s’est déroulée a créé un nouveau concept de culture « Microbial Culturomics » qui a permis d’isoler 193 nouvelles espèces bactériennes anaérobies. Un travail sur l’utilisation des antioxydants pour permettre la culture aérobie des bactéries anaérobies a également été amorcé : une optimisation des techniques de culture prometteuse autour de laquelle mes travaux ont vu le jour. Notre premier projet a consisté à développer un dispositif de culture innovant permettant la culture des archaea méthanogènes en aérobiose et en absence de source externe de dihydrogène. Notre deuxième projet a consisté à élaborer un flacon d’hémoculture unique dans lequel la croissance de toutes les bactéries, aérobies et anaérobies, pouvaient être détectées. Notre troisième projet quant à lui repose sur la comparaison du mode de culture anaérobie et de celui en aérobie avec les antioxydants à travers l’exemple de trois souches bactériennes strictement anaérobies. L’utilisation des antioxydants pour faciliter la culture des microorganismes anaérobies a donc apporter des résultats très prometteurs qui pourrait être utilisés, après validation par des études multicentriques dans les laboratoires de microbiologie clinique et environnementaux
Anaerobic microorganisms are characterized by their ability to grow and survive in the absence of oxygen. Indeed free oxygen molecules are not used for their metabolism and can be toxic to varying degrees, sometimes leading to cell death. Although it is known that these microorganisms are the predominant in our digestive microbiota and that they have a great impact on our health, their culture remain long, fastidious, costly, and in most cases impossible. Becteria culture is an indispensable tool for isolating strains, performing studies from living models, and identifying new ones. Thus, the laboratory in which my thesis tooks place created a new concept of culture "Microbial Culturomics" which made it possible to isolate 193 new anaerobic bacterial species. A work based on the use of antioxidants to enable the aerobic culture of anaerobic bacteria was also initiated: a promising optimization of the culture techniques from which my work was born. Our first project consisted in developing an innovative culture device allowing the cultivation of methanogenic archaea in aerobic and without an external source of dihydrogen. In our second project, we performed a single culture bottle in which the growth of all bacteria, aerobic and anaerobic, could be detected. Our third project was based on the comparison of anaerobic and aerobic culture with antioxidants through the example of three strictly anaerobic bacterial strains.Therefore the use of antioxidants enable to facilitate anaerobic bacteria cultivation. These results are very encouraging for clinical and environmental microbiology laboratories

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Royet, David. "Nouvelle approche de décryptage de la diversité bactérienne environnementale par capture magnétique de populations spécifiques de bactéries au sein de microbiotes complexes." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEC013/document.

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Les bactéries, organismes les plus abondants de notre planète, ont un rôle fondamental dans le fonctionnement des écosystèmes. En dépit de leur importance, la caractérisation des communautés bactériennes (microbiotes) demeure encore aujourd’hui très incomplète. Ceci a pour origine l’impossibilité de complètement décrypter taxonomiquement et fonctionnellement les microbiotes de ces écosystèmes et donc à appréhender la diversité bactérienne dans son ensemble que ce soit par des approches culturales (avec seulement 1% de bactéries cultivables) ou par des approches metagénomiques limitées par les biais d’extraction, de séquençage et d’analyse. Les travaux entrepris dans le cadre de cette thèse visent à développer une nouvelle voie exploratoire passant par le fractionnement des microbiotes afin d’en étudier séparément les génomes des différentes populations ou groupes de populations, leur somme devant permettre de reconstituer un metagénome complet. Cet objectif requiert le développement d’un outil pour la sélection spécifique de bactéries (sur des critères taxonomiques ou fonctionnels) et leur isolement du reste des microorganismes non ciblés. Les travaux de thèse ont porté sur le développement d’une approche de marquage magnétique des bactéries basée sur l’hybridation moléculaire (hybridation in situ) complétée par celui d’un outil de tri microfluidique. Deux méthodes ont été développées, MISH et HCR, ciblant le gène de l’ARNr 23S, chacune reposant sur la formation, lors du processus d’hybridation, d’une structure secondaire en arborescence (MISH) ou ordonnée (HCR) permettant le greffage de nanoparticules magnétiques. Les résultats obtenus illustrent le potentiel des deux approches d’abord pour le marquage spécifique de bactéries cibles (E.coli et Pseudomonas putida) en conditions de culture au laboratoire puis dans un second temps dans des échantillons de sol. Le tri microfluidique a également été optimisé par le développement d’un nouveau dispositif de tri magnétique permettant la séparation des cellules marquées sous flux continu faisant appel à l’injection d’un polymère composite magnétique pour intégrer au fond du microcanal une série de bandes parallèles magnétiques. La fonctionnalité du dispositif a été démontrée, sa simplicité de fabrication en faisant un outil de choix pour une application en routine dans les laboratoires d’écologie microbienne. En dépit de résultats prometteurs toute cette nouvelle approche d’étude de la diversité bactérienne environnementale nécessite encore de nombreuses étapes d’optimisation
Bacteria, the most abundant organisms on our planet, have a fundamental role in ecosystem functioning. Despite their importance, the characterization of bacterial communities is today still incomplete. This is due to the impossibility of completely decomposing taxonomically and functionally the microbial communities of these ecosystems and as a consequence to apprehend the whole bacterial diversity, either by cultural approaches (with only 1% of culturable bacteria) or by metagenomic, a limited approaches cause by biases in extraction, sequencing and analysis. The work undertaken in this thesis aims to develop a new exploratory pathway through the fractionation of microbiota in order to study separately genomes of different populations or groups of populations. Their sum should enable reconstitution of complete metagenome. This objective requires the development of a tool for the specific selection of bacteria (on taxonomic or functional criteria) and their isolation from the rest of the non-target microorganisms. The thesis work focused on the development of a magnetic labeling approach for bacteria based on molecular hybridization (in situ hybridization) complete by development of a microfluidic cell-sorting tool. Two methods have been developed, MISH and HCR, targeting the 23S rRNA gene, each based on the formation, during the hybridization process, of a secondary random structure (MISH) or organized structure (HCR) enabling binding to magnetic nanoparticles. Results obtained illustrate the potential of the two approaches initially for the specific labeling of target bacteria (E.coli and Pseudomonas putida) under laboratory conditions and then in soil samples. The microfluidic sorting was also optimized by the development of a novel magnetic cell-sorting device allowing the separation of the labeled cells under continuous flow using the injection of a magnetic composite polymer to integrate a series of magnetic parallel strips at the bottom of the microchannel. The proper functioning of the sorting device has been demonstrated, its simple production making it a tool of choice for a routine application in laboratories of microbial ecology. Despite promising results all this new approach for studying environmental bacterial diversity is still requiring many optimization steps

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Guet-Revillet, Hélène. "Métagénomique bactérienne de l'hidrosadénite suppurée." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T065/document.

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L’hidrosadénite suppurée (HS) ou maladie de Verneuil, est une maladie cutanée orpheline fréquente qui touche 1 % de la population générale. Elle se manifeste par des lésions inflammatoires récidivantes ou chroniques des plis axillaires, inguinaux et périnéaux. La sévérité clinique de la maladie varie selon les patients. Les lésions les moins sévères (lésions de stade 1 dans la classification de sévérité clinique de Hurley) sont des nodules inflammatoire centimétriques pouvant évoluer vers l’abcédation. Les lésions les plus sévères (lésions de stade 2 et 3 de Hurley) sont des lésions suppurées étendues et chroniques. Sur le plan histologique, la lésion primitive de l’HS semble être une hyperplasie de l’épithélium du follicule pileux. La physiopathologie de la maladie est mal connue et probablement multifactorielle, incluant des facteurs génétiques, hormonaux, infectieux et dys-immunitaires. Il a été montré récemment qu’une antibiothérapie à large spectre pouvait permettre d’obtenir une rémission clinique prolongée des lésions inflammatoires de l’HS. Objectif du travail : L’objectif principal de ce travail était d’identifier par des techniques de culture classique et de métagénomique bactérienne les espèces ou les flores bactériennes spécifiquement associées aux lésions d’HS des trois stades de sévérité clinique. Résultats : Nous avons identifié par culture bactérienne deux profils bactériens lésionnels. Le premier était représenté par Staphylococcus lugdunensis, et plus rarement par d’autres espèces bactériennes de la flore cutanée commensale (Propionibacterium acnes, staphylocoques à coagulase négative et Staphylococcus aureus). Le second correspondait à une flore anaérobie composée de bactéries anaérobies stricts, d’Actinomycetes et de streptocoques du groupe milleri. L’approche métagénomique a permis d’identifier les germes anaérobies stricts associés aux lésions : des cocci à Gram positif de la flore cutanée (principalement Anaerococcus spp., Peptoniphilus spp., Finegoldia spp.) des bacilles à Gram négatif anaérobies n’appartenant pas à la flore cutanée (Prevotella spp., Porphyromonas spp., Fusobacterium spp), Veillonellaceae et Corynebacteriaceae. Ce profil était caractéristique des lésions suppurées chroniques de stade 2 et 3 et était également associé à certaines lésions de stade 1. Les lésions des stades 2 et 3 présentaient une diversité bactérienne supérieure à celle des lésions de stade 1, avec un nombre plus élevé de taxons très minoritaires dans la flore cutanée (Fusobacteria, Bacteroidetes, Peptococcaceae, Erysipelotrichales). Conclusion : Cette étude démontre que certaines espèces bactériennes sont spécifiquement associées aux lésions d’HS. Ces espèces sont impliquées dans des infections cutanées, mais aussi dans des infections sévères, ce qui témoigne de leur pathogénicité. L’efficacité des antibiotiques chez les patients et les résultats de cette étude suggèrent qu’un processus infectieux participe à la présentation clinique de l’HS. Notre hypothèse est que ces infections surviennent en raison d’une anomalie primitive de la barrière cutanée folliculaire
Hidradenitis suppuratiav (HS) is an orphan skin inflammatory disease disease characterized by chronic or recurrent inflammatory lesions localized in the armpits, the inguinal and perineal folds. With a 1% prevalence of a general population, HS is an public health issue. The clinical severity of the disease is heterogeneous among patients. Most patients present the mild form of the disease with inflammatory nodules and abscesses (Hurley stage 1 lesions). More severe patients show extended chronically suppurating lesions (Hurley stage 2 and Hurley stage 3 lesions). The primary histological lesion of HS is characterized by epidermal follicular hyperplasia and perifollicular inflammation. The physiopathology of HS remains unclear. HS is probably a multifactorial disease, involving genetical, immunological and infectious factors. Indeed, wide-spectrum antibiotic treatments can significantly improve or induce prolonged clinical remissions of HS inflammatory lesions. Objective: The main objective of this work was to identify the bacterial species or flora specifically associated with Hurley stage 1, 2 and 3, using prolonged aerobic and anaerobic culture and bacterial metagenomics (454 sequencing of 16Sr DNA libraries). Results. Using bacterial culture, we identified two bacterial profiles associated with HS lesions . The first one was represented by Staphylococcus lugdunensis and rarely by other skin commensals (Propionibacterium acnes, coagulase negative staphylococci and Staphylococcus aureus). Results. The second one corresponded to a mixted anaerobic flora including strict anaerobes, Actinomycetes and milleri group streptococci. The metagenomic approach allowed to identify the anaerobic flora associated with lesions : Gram positive cocci from the cutaneous flora (mainly Anaerococcus spp., Peptoniphilus spp., Finegoldia spp.) and Gram negative rods which do not belong to the cutaneous microbiota (Prevotella spp., Porphyromonas spp., Fusobacterium spp), Veillonellaceae and Corynebacteriaceae. This profile was typically associated with Hurley stage 2 and 3 lesions but was also observed in Hurley stage 1 lesions. Hurley stage 2 and 3 lesions presented an increased bacterial diversity as compared to Hurley stage 1 lesions, with a higher number of taxa taxa rarely associated with normal skin microbiota (Fusobacteria, Bacteroidetes, Peptococcaceae, Erysipelotrichales). Conclusion. This study demonstrate that particular bacterial species are specifically associated with HS lesions. These species are cause soft tissue and skin infections, but also in severe infections arguing for their pathogenicity. These data provide a rationale for antibiotic use in HS, and suggests that the disease may be due to a primitive immune defect of the follicular skin barrier

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Groh, Chloé. "Deciphering the interactions between plants and bacteria in the context of isoprenoid biosynthesis in Arabidopsis thaliana." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAJ079.

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Les isoprénoïdes constituent une grande classe de molécules que l'on retrouve chez tous les organismes vivants et qui sont impliquées dans divers processus biologiques. Le but de ma thèse était de déterminer si ces molécules pouvaient être impliquées dans les interactions entre plantes et bactéries. J'ai travaillé sur des plantes Arabidopsis thaliana sauvages, et sur deux mutants affectés dans chacune des deux voies de biosynthèse des isoprénoïdes existant chez les plantes supérieures. Un inventaire des communautés constituant le microbiote de ces plantes a mis en évidence certaines bactéries dont l’abondance varie dépendamment du génotype, malgré l'existence d'un microbiote commun entre plantes sauvages et mutantes. De plus, il a été démontré que les plantes affectées dans la voie de biosynthèse plastidiale, dite du méthylérythritol phosphate (MEP), sont plus sensibles que les plantes sauvages à l’infection par Pseudomonas syringae, un phytopathogène bien connu. Ensemble, ces résultats suggèrent que les isoprénoïdes peuvent jouer un rôle dans les interactions entre plantes et bactéries. D’autre part, 230 souches interagissant avec A. thaliana ont été isolées au laboratoire, parmi lesquelles certaines ont été testées pour déterminer leur effet sur le phénotype et la résistance des plantes à P. syringae, ainsi que l’effet des isoprénoïdes sur ces souches
Isoprenoids are a large class of molecules found in all living organisms that are implicated in diverse biological processes. The aim of my thesis was to decipher if they could be involved in the interactions between plants and bacteria. Therefore, I worked on Arabidopsis thaliana wild-type and mutants, altered in the two isoprenoid biosynthesis pathways occurring in higher plants. An inventory of the communities interacting with wild-type and mutants highlighted some differentially abundant bacteria, despite the existence of a core microbiota. In addition, plants affected in the plastidial biosynthesis pathway, referred as the methylerythritol phosphate (MEP) pathway, have been shown to be more affected than wild-type by Pseudomonas syringae, a well-known phytopathogen. Together, these results suggest that isoprenoids may play a role in the interactions between plants and bacteria. In addition, 230 strains were isolated from A. thaliana in the laboratory, among which some of them were tested for their impact on the plant fitness and resistance to P. syringae, and for the impact on isoprenoids on these strains

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Goma, Loemba Roll. "Interactions ver de terre-bactéries au cours du transit intestinal." Thesis, Paris Est, 2010. http://www.theses.fr/2010PEST0026.

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Outre ses activités de bioturbateur et d'ingénieur de l'écosystème, l'impact du ver de terre sur le sol pourrait être fortement lié à d'autres processus dépendant du transit du sol dans son tube digestif. En particulier, l’interaction entre le ver de terre et les bactéries au cours du transit digestif demeure mal établie, malgré un certain nombre de travaux. Chez 3 espèces de vers de terre tempérées, Lumbricus terrestris, Dendrobaena veneta et Aporrectodea caliginosa, appartenant à 3 catégories écologiques différentes (épigé, anécique, endogé), on montre par DGGE ARN 16S culture-indépendante, que la structure in vivo des communautés bactériennes du tube digestif est très différente de celle du sol et qu'elle varie d'une partie à l'autre du tube digestif. En effet, chez les 3 espèces de vers de terre, les parties antérieures du tube digestif (jabot-gésier et intestin antérieur) apparaissent comme les sites d'intensité maximum des perturbations de la structure des communautés bactériennes du sol ingéré, tandis que dans les parties postérieures, la structure des communautés se rapproche de celle du sol. Les extraits hydrosolubles du tube digestif, caractérisés par leur teneur en protéines, sucres reducteu rs, glucose et sucres aminés, présentent une évolution quantitative et qualitative parfaitement superposable à celle de la structure des communautés bactériennes observées in vivo, avec des teneurs en protéines et sucres réducteurs hydrosolubles très élevées (jusqu'à 270 µg/mg de poids sec du contenu du tube digestif chez L. terrestris) dans les parties antérieures du tube digestif (jabot-gésier et intestin antérieur) mais qui déclinent brusquement dans les parties postérieures (intestins moyen et postérieur). La simulation in vitro de l'effet des extraits hydrosolubles du tube digestif sur un sol démontre leur capacité à modifier la structure des communautés bactériennes dominantes du sol chez les 3 espèces de vers de terre étudiés. Leur effet, particulièrement visible avec les hydrosolubles issus du jabot-gésier et de l'intestin antérieur, diminue ou disparaît avec les hydrosolubles extraits de l'intestin moyen et postérieur. En perspectives, à partir de ces résultats, le concept des épargnes microbiennes est proposé pour décrire comment l'énergie disponible du sol (biomasse microbienne) pourrait être utilisée, transmise et maintenue dans le tube digestif.Mots clés : sol, tube digestif, ver de terre, microbiote, bactéries, DGGE ARN 16S, résilience, épargnes microbiennes, mutualisme
In addition to bioturbation and ecosystem engineer activities, the impact of earthworms on the soil could be strongly linked to other processes dependent on transit of soil through his digestive tract. In particular, the interaction between earthworm and bacteria during digestive transit remains poorly established, although a number of works. In three species of temperate earthworm, Lumbricus terrestris, Dendrobaena veneta et Aporrectodea caliginosa, belonging to three different ecological categories (epigeic, anecic, endogeic), we show by culture-independent DGGE 16S RNA, the structure in vivo of digestive tract bacterial communities is very different from that of the soil and varied from one part to another of the digestive tract. Indeed, among the three species of earthworms, the anterior parts of the digestive tract (crop-gizzard and foregut) appear as sites of maximun intensity disturbances in bacterial community structure of soil ingested , while in posterior parts (midgut and hindgut), the community structure is more similar to that of the soil. The water-soluble extracts of the digestive tract, characterized by their protein, reducing sugars, glucose and amino sugars content, present a quantitative and qualitative change perfectly correlated with the bacterial community structure observed in vivo, with very high quantities of soluble protein and reducing sugars (up to 270 µg/ mg dry weight of gut contents of L. terrestris) in the anterior parts of the digestive tract (crop-gizzard and foregut) but declined sharply in the posterior parts (midgut and hindgut). The in vitro simulation of the effect of soluble extracts of the digestive tract of a soil demonstrates their ability to alter the dominant bacterial community structure of soil in three species of earthworms studied. Their effect, particularly visible with the water-soluble extracts from crop-gizzard and foregut, decreases or disappears with water-sol uble extracts of the midgut and hindgut. In perspective, from these results, the concept of microbial savings is proposed to describe how the energy available in the soil (microbial biomass) could be used, transmitted and maintained in the digestive tract.Keywords: soil, gut, earthworm, microbiota, bacteria, DGGE 16S RNA, resilience, microbial savings, mutualism

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Lopes, Helena de Fátima Silva. "Microbiome of Pinus pinaster." Master's thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/16427.

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Mestrado em Microbiologia
Pinus pinaster has a great environmental, historical and economical importance to Portugal. It represents the third place in occupation in forestry area. However, it has been losing area due to the modifications on land use, fires and diseases such as the pine wilt disease (PWD). Native from the North America the PWD has been spreading worldwide, it has spread through Asia and more recently was identified in Europe being detected in Portugal in 1999, representing a major threat to forests. Recently, the importance of the bacteria community to the PWD has been accessed and few studies address the microbiome of P. pinaster. Most of the existing studies uses culture-dependent techniques. This work aimed to reveal the bacterial community of healthy P. pinaster trees using culture-independent techniques. To observe the bacterial communities of healthy P. pinaster, stem samples from trees aged between 20 and 30 years were collected from 4 Portuguese locations: Comporta, Góis, Madeira Island and Vouzela. The trunks were cut into disks and the sawdust of the center of these disks were used to extract DNA. Samples were tested for the presence of the PWD nematode and all were negative. DGGE analysis was performed to compare the bacterial community of different samples and pyrosequencing was used to identify the community. After analyzing the DGGE profiles, a sample was cloned and sequenced, and the results showed that the most common and intense bands belonged to chloroplast genetic material. Pyrosequencing results had a great amount of reads belonging to chloroplast and they were eliminated from the study. With the pyrosequencing, six plyla were detected: Proteobacteria, Acidobacteria, Firmicutes, Bacteriodetes, Armatimonadetes and Actinobacteria. Proteobacteria was the most common, and from this plylum, Gammaproteobacteria was the most abundant class. Samples grouped by location and the location community differ significantly, only two OTUs were shared by all locations. Despite the low read number the bacterial community was characterized, and this information can be used for future studies.
Pinus pinaster possui uma grande importância ambiental, histórica e económica em Portugal, conquistando o terceiro lugar em ocupação florestal. Entretanto sua área está a diminuir devido a modificações na utilização dos terrenos, fogos e doenças como a da murchidão do pinheiro (DMP). Nativa da América do Norte, a DMP vem se espalhando em uma escala global, já está presente na Ásia e mais recentemente na Europa, sendo detectada em 1999 em Portugal, representando assim uma ameaça a florestas do mundo inteiro. Existem evidências que apontam para a importância da comunidade bacteriana no desenvolvimento da DMP e poucos estudos abordam o microbioma do P. pinaster, com a maioria utilizando metodologias baseadas em cultivo. Este trabalho tem como objetivo revelar a comunidade bacteriana de árvores de P. pinaster saudáveis utilizando técnicas independentes de cultivo. Para observar a comunidade bacteriana do P. Pinaster saudável, árvores entre 20 e 30 anos de idade foram recolhida de 4 localidades portuguesas: Comporta, Góis, Ilha da Madeira e Vouzela. O tronco dessas árvores foi cortado em discos e o serrim do centro desses discos foi utilizado para extração de DNA. Todas as amostras foram testadas para a presença do nemátodo sendo que este estava ausente em todas as amostras. Foi feito DGGE com o objectivo de comparar a comunidade bacteriana de diferentes amostras, e esta foi identificada utilizando-se pirosequenciação. Tendo em conta os perfis de DGGE, foi feita a clonagem e sequenciação de uma das amostras, e verificou-se que as bandas mais intensas, e presentes em todas as amostras, eram material genético proveniente de cloroplastos. Os resultados de pirosequenciação revelaram uma grande quantidade de reads proveniente de cloroplastos que foram eliminadas do estudo. A análise dos resultados da pirosequenciação permitiu identificar seis filos: Proteobacteria, Acidobacteria, Firmicutes, Bacteriodetes, Armatimonadetes e Actinobacteria. Proteobacteria foi o filo mais comum e dele Gammaproteobacteria foi a classe mais abundante. As amostras se agruparam de acordo com o local de origem e as comunidades dos locais se diferenciavam significativamente. Apenas duas OTUs eram compartilhadas por todos os locais. Apesar do baixo número de reads, a estrutura da comunidade bacteriana foi caracterizada e essa informação pode ser agora utilizada em futuros estudos.

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Donatin, Emilie. "Détection des bactéries entéropathogènes : approche polyphasique." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5034/document.

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Le corps humain est un ensemble de microflores où cohabitent bactéries, archées, virus et eucaryotes. Ces écosystèmes complexes sont appelés microbiotes. Parmi ceux-ci figure le microbiote intestinal qui compte 1011 à 1014 bactéries/g de selle. Les modifications de la flore intestinale peuvent être à l'origine de pathologies comme les diarrhées infectieuses. Il s'agit d'un véritable problème de santé publique puisqu'environ 2.16 millions de décès sont liés à cette pathologie chaque année. Les virus intestinaux jouent un rôle prépondérant mais les infections bactériennes restent également importantes. Le diagnostic de ces infections bactériennes reste compliqué puisque le microbiote intestinal comporte 75% d'espèces non cultivables. De plus, on ne dispose pas réellement d'une liste exhaustive des bactéries pouvant être responsables de diarrhées infectieuses. Nous avons donc choisi d'étudier le microbiote intestinal dans des selles normales et pathologiques, par une approche polyphasique alliant une étape préliminaire de concentration des selles diarrhéiques par la lyophilisation, à des techniques de culture et des méthodes de biologie moléculaire. Pour cela nous avons mis au point une nouvelle technologie pour la détection des entéropathogènes par hybridation sur puce à ADN permettant la détection des bactéries et des virus ADN entéropathogènes, en présence d'un témoin archae. Notre outil permet le diagnostic multiplexe des diarrhées infectieuses puisque nous avons correctement identifié un adénovirus et la bactérie Campylobacter jejuni présents dans une même selle
The human body is a collection of microflora where cohabit bacteria, archaea, viruses and eukaryotes. These complex ecosystems are called microbiota. Among these is the intestinal microbiota that counts 1011 to 1014 bacteria/g of stool. Changes in the intestinal flora can cause of pathologies such as infectious diarrhea. This is a real public health problem since about 2.16 million deaths are related to this disease each year. Enteric viruses play a preponderant role but bacterial infections are also important. The diagnosis of bacterial infections is complicated because the intestinal microbiota includes 75% non-cultivable species. In addition, there is not really a list of bacteria could be responsible for infectious diarrhea. We therefore decided to study the intestinal microbiota in normal stool and also pathological stools by a polyphasic approach combining a preliminary step of diarrheal stools concentration by lyophilization, with cultivation techniques and molecular biology methods. We developed a new technology for the detection of enteropathogens by hybridization on DNA microarray for the detection of bacteria and enteric viruses (DNA) in the presence of a control archaea. Our tool allows multiplexed diagnostic of infectious diarrhea since we correctly identified an adenovirus and Campylobacter jejuni present in a same sample. This is the first DNA microarray for multiplex detection of bacteria and viruses (DNA) enteropathogens. An improvement of our protocol for nucleic acid extraction is proposed to allow the detection of RNA viruses such as rotavirus and calicivirus which are currently dominant

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Hoffmann, Christian. "Integrating the archaea, bacteria and fungi of the gut microbiome with human diet." Universidade Federal de Goiás, 2013. http://repositorio.bc.ufg.br/tede/handle/tede/3160.

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A dieta influencia a saúde sendo uma fonte de nutrientes e toxinas, e por moldar a composição de populações microbianas residentes no corpo humano. Estudos prévios começaram a mapear as associações entre a dieta e bactérias e vírus do microbioma intestinal humano. Este trabalho investiga as associações entre a dieta e populações arqueanas e fúngicas, tomando vantagem de amostras oriundas de 98 indivíduos bem caracterizados, e integra esses dados novos com o conhecimento corrente relacionado a bactérias e o microbioma intestinal humano. A dieta foi quantificada utilizando questionários que acessam a dieta usual e recente, e arquêas e fungos foram caracterizados usando genes marcadores obtidos de amostras fecais através e sequenciamento de DNA em larga escala de última geração. Foram encontrados 66 gêneros de fungos, geralmente com uma presença mutuamente exclusiva dos filos Ascomycota e Basidiomycota. Quanto as arquêas, Methanobrevibacter foi o gênero mais prevalente, presente em 30% das amostras. Diversas outras arquêas foram detectadas com abundancia e frequência mais baixa. Uma miríade de associações foi observada entre fungos e arquêas e a dieta, entre fungos e arquêas, e entre estes e linhagens bacterianas. Metanobrevibacter e Candida foram positivamente associados com uma dieta rica em carboidratos, e negativamente com dietas ricas em amino acidos, proteínas e ácidos graxos. Dados publicados previamente enfatizam que a estrutura das populações bacterianas no intestino são primariamente com hábitos alimentares de longo prazo, porém, uma abundancia alta de Candida foi fortemente associada com a ingestao recente de carboidratos. A abundância de Methanobrevibacter foi associada tanto com a ingestão usual ou recente de carboidratos. Estes resultados confirmam estudos direcionados anteriores e provém varias novas associações a serem consideradas quando modelando os efeitos da dieta no microbioma intestinal e a na saúde humana.
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. This work investigates associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals, and integrates this novel data with the current knowledge regarding the bacteria of the human gut microbiome. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacterwas the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter andCandida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. Previously published data emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

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Drissi, Fatima. "Rôle des bactéries dans l'obésité : implication des génomes d'espèce Lactobacillus dans la prise de poids." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM5034.

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Il a été montré que la consommation de Lactobacillus pouvait avoir des conséquences sur le poids de l’hôte, et ce, en fonction de la souche inoculée. Nous avons voulu comprendre le mécanisme par lequel ces microorganismes prolifèrent dans le tube digestif et induisent un changement de poids. Nous avons exploré la production de bactériocines permettant aux souches de Lactobacillus de croître au détriment des autres micro-organismes. Nous avons constitué une base de données de bactériocines nommée BUR et recherché les bactériocines dans les génomes de bactéries du tube digestif humain. Nous avons observé une abondance de bactériocines dans les génomes des bactéries du tube digestif, majoritairement dans les Firmicutes. Aussi, nous avons approfondi l’étude du profil métabolique des souches de Lactobacillus par une approche génomique et dans une analyse in vitro. Nous avons constaté que les souches de Lactobacillus dont la consommation induit une perte de poids possèdent des enzymes qui empêchent l'obésité en réduisant les niveaux de glucose dans le sang, les niveaux de triacylglycérols sériques, la masse corporelle et l'accumulation de graisse, tandis que les génomes des souches dont la consommation induit un gain de poids codent pour plusieurs enzymes favorisant la production de fructose, et mobilisent l'énergie et le carbone stocké dans les acides gras. De ce fait, nous pouvons dire que les espèces de Lactobacillus jouent un rôle important dans la digestion des nutriments, avec un effet direct sur le changement de poids
It has been shown that Lactobacillus consumption could affect the weight of the host, and led consequently to significant weight gain or loss, depending on the strain. We wanted to understand the mechanism by which these microorganisms induce weight change. We explored the various known mechanisms, including the production of bacteriocins, allowing Lactobacillus strains to grow at the expense of other microorganisms. We established a bacteriocin database, named BUR, and search for bacteriocins in the genomes of human gut bacteria. We observed an abundance of bacteriocins in the genomes of bacteria in the digestive tract, predominantly in Firmicutes. We also have deepened the study of the metabolic profile of Lactobacillus strains, both by a genomic approach and in an in vitro assay, to better understand the pathophysiology of obesity. We have found that Lactobacillus strains whose consumption induces weight loss possess enzymes which prevent obesity by reducing glucose levels in blood, serum triacylglycerols levels, body weight and the accumulation of fat, whereas the genomes of strains whose consumption leads to weight gain encode several enzymes promoting the production of fructose and mobilize energy and the carbon stored in the fatty acids. Therefore, we can say that Lactobacillus species are important in the digestion of nutrients and can have a great influence on carbohydrate and lipid metabolism, with direct effect on weight change

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Cambon, Marine. "Heterogeneity within infections : the case of the vector-borne insect pathogen, Xenorhabdus nematophila." Thesis, Toulouse 3, 2018. http://www.theses.fr/2018TOU30308.

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De nombreuses études ont jusqu'ici considéré les infections comme étant des interactions deux-à-deux, entre un hôte et un pathogène, minimisant ainsi la complexité du processus infectieux. En effet, les infections sont souvent très hétérogènes, menant à des interactions plus complexes. Au cours de ce travail, nous cherchons à répondre à deux questions: (i) La transmission d'un pathogène peut-elle être impactée lorsque de l'hétérogénéité phénotypique apparaît dans sa population au cours de l'infection ? (ii) Comment les pathogènes interagissent-ils avec la communauté bactérienne généralement associée à l'hôte avant l'infection ? Pour étudier ces questions, nous nous sommes intéressés à Xenorhabdus nematophila, une bactérie pathogène d'insectes transmise par un vecteur, le némaotde Steinernema carpocapsae. Au cours d'une infection par X. nematophila, différentes sous-populations ayant différentes caractéristiques phénotypiques sont produites. Nous avons cherché à déterminer les mécanismes moléculaires responsables de cette diversification phénotypique, ainsi que sa potentielle valeur adaptative pour X. nematophila. Nous avons montré que certaines de ces formes phénotypique sont des mutants qui semblent être sous forte sélection positive au cours de l'infection. À l'inverse, ces mutants ont un impact négatif sur la reproduction du vecteur nématode, ce qui réduit leur transmission. La dynamique d'hétérogénéité phénotypique chez X. nematophila semble donc déterminée par des pressions de sélections contraires à court terme et à long terme. La production de molécules anti-microbiennes chez X. nematophila devraient lui permettre de dominer la communauté bactérienne à l'intérieur de l'insecte et faciliter sa ré-association avec son vecteur. Nous avons donc décrit la composition de la communauté microbienne présente dans des insectes morts d'une infection par X. nematophila, et montré qu'en dépit de sa production d'antibiotiques, X. nematophila est loin de dominer la communauté microbienne après la mort de l'insecte. Elle cohabite avec des bactéries provenant à la fois du microbiote de l'hôte insecte, et de celui du vecteur nématode. Cela soulève de nombreuses questions sur le rôle d'autres microorganismes dans les interactions Xenorhabdus-Steinernema, et sur leur influence dans l'évolution de cette symbiose mututaliste
Numerous studies have considered infections as pairwise interactions between a single pathogen and its host, sometimes leading to an incomplete picture of infectious processes. In this work, we focused on more complex types of interactions that arise because infections are usually heterogeneous. More precisely, we have investigated two main issues: (I) how pathogen transmission is impacted by phenotypic heterogeneity which arises within the pathogen population during the infection, and (ii) how do pathogens interact with the bacterial community which is naturally associated to the host before infection? To assess these questions, we have been studying Xenorhabdus nematophila, an insect-killing bacterial pathogen which is transmitted by a nematode vector, Steinernema carpocapsae. One interesting feature of X. nematophila is that it produces different sub-populations during the course of an infection, each one having distinctive phenotypic features (e.g. one form produces antibiotics and is mobile, while the other does not produce antibiotics nor flagella). In this work, we first tried to identify the molecular mechanisms responsible for this diversification of phenotypes, and tested if phenotypic heterogeneity in X. nematophila has some adaptive value. We showed that some of these phenotypic forms were mutants, which seem to be under strong positive selection during infection. We also showed, however, that these mutants impair nematodes reproduction, which in turn reduces transmission. Therefore, the dynamics of phenotypic heterogeneity in X. nematophila seems to be determined by contradictory short-term and long-term selective pressures. A second interesting feature of X. nematophila is that it produces a lot of antimicrobial compounds which should allow it to dominate the bacterial community inside the insect it has killed. This can be key to ensure the re-association of X. nematophila with its nematode vector inside the insect cadaver. We investigated the bacterial composition of the microbial communities present in insects cadavers after infection by X. nematophila. We found that despite the numerous antibiotics it is able to secrete, X. nematophila is far from dominating microbial community after host death. It rather cohabits with microorganisms from the microbiota of both the insect host and the nematode vector. This raises numerous questions about the impact of these other microorganisms on Xenorhabdus-Steinernema interactions, and therefore on their potential influence on how this mutualistic association has evolved

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Minard, Guillaume. "Écologie du microbiote bactérien associé au moustique tigre Aedes albopictus : une approche "omique" pour l'exploration de l'holobionte vecteur." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10299/document.

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Originaire d'Asie du Sud et de l'Est, le moustique tigre Aedes albopictus est aujourd'hui implanté sur 5 des 6 continents et les moyens de lutte mis en place pour l'éliminer peinent à freiner son expansion. Ces dernières années, l'étude des communautés microbiennes associées aux insectes a permis de démontrer leur implication dans des fonctions clefs de la biologie de leurs hôtes (nutrition, immunité, résistance aux stress biotiques et abiotiques …). Ensemble, ils constituent un super-organisme appelé holobionte. Ainsi, une meilleure connaissance de l'écologie microbienne d'Ae. albopictus pourrait nous apporter de nouvelles perspectives dans la compréhension du fonctionnement du pathosystème vectoriel. C'est dans ce contexte que s'est inscrit mon projet de thèse qui a consisté à décrire le microbiote bactérien du moustique tigre en lien avec son écologie et la génétique de ses populations. Nos travaux se sont tout d'abord portés sur des exemples précis d'interactions avec des symbiotes d'intérêts puis nous avons élargi cette étude à l'ensemble des communautés bactériennes et leurs facteurs de variation, en bénéficiant du développement des nouvelles technologies de séquençage. Les résultats obtenus ouvrent la voie vers de nouvelles hypothèses sur le fonctionnement et la dynamique de l'holobionte moustique avec la prise en compte des interactions symbiotiques comme un élément majeur du pathosystème vectoriel
Originated from South East Asia, the Asian tiger mosquito Aedes albopictus is now established on 5 of the 6 continents. Control strategies to limit its introduction and expansion remain restricted. Those last years, studies on insect microbial communities highlighted the key role of symbionts in the biology of their hosts (nutrition, immunity, resistance to biotic and abiotic stresses…). Together, they constitute a super-organism called the holobiont. Therefore, a better knowledge of microbial ecology of Ae. Albopictus should increase the understanding of vectorial pathosystem. In this context, my thesis project consisted to improve the description of bacterial microbiota associated with the Asian tiger mosquito in relation with its ecology and population genetics. We first based our attention on specific models of symbiotic interactions and then we extended our study to the whole bacterial community and its variation factors using high throughput sequencing technologies. Our results open the way to new hypotheses about the function and dynamics of mosquito holobionte taking into account the symbiotic interactions as a major component of the vectorial pathosystem

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Mansos, Lourenço Marta. "Deciphering in vivo efficacy of virulent phages in the mammalian gut." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS260.pdf.

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L'intestin des mammifères est peuplé de nombreux et divers microbes comprenant des bactéries et leurs prédateurs viraux, des bactériophages (phages). Les interactions entre les phages et les bactéries intestinales sont encore mal comprises. Des expériences indépendantes ont montré que les phages virulents n’avaient aucun effet majeur sur l’abondance des bactéries intestinales ciblées, en dépit de leur amplification durable. Cela suggère que des facteurs encore inconnus de l'environnement intestinal modulent ces interactions. À l’aide d’une analyse transcriptomique comparative de la bactérie Escherichia coli cultivée in vitro et in vivo (dans l’intestin de mammifères), nous avons constaté que, dans l’intestin, les bactéries réduisent l’expression de gènes liés aux récepteurs du phage. Ceci permet d’expliquer l’absence de sélection des bactéries mutées devenues résistantes aux phages lors d'expériences in vivo. D’autre part, nous avons montré que l'acquisition d'un îlot de pathogénicité, souvent associé aux souches intestinales humaines d'E. coli, affecte la susceptibilité aux phages en régulant négativement un mécanisme de défense contre l'ADN étranger. Enfin, nous avons examiné la répartition des phages et des bactéries dans les parties mucosales et luminales de l’intestin et avons observé une distribution spatiale hétérogène de ces deux populations antagonistes, corroborant l'hypothèse d'une dynamique « source-sink ». Globalement, nos données démontrent que de multiples facteurs incluant la distribution spatiale, la physiologie bactérienne et les défenses contre l’ADN étranger modulent les interactions entre bactéries et phages dans l’intestin des mammifères
The mammalian gut is a heterogeneous environment inhabited by a large and diverse microbial community, including bacteria and their viral predators, bacteriophages (phages). Dynamic interactions between virulent phages and bacteria in the gut are still poorly understood, which is also an obstacle for the design of successful therapeutic interventions based on phages. Independent experiments have shown that virulent phages were found to have no major effects on their targeted bacteria in the gut, in spite of sustainable phage amplification. This suggests that there are unknown factors in the gut environment that modulate these interactions. Using comparative transcriptomics analysis of E. coli grown in vitro and in vivo (within the mammalian gut) we found that in the gut, bacteria downregulate the expression of genes related to phage receptors, which provides an explanation for the lack of selection of phage-resistant bacteria during in vivo experiments. We also found that the acquisition of a pathogenicity island commonly found in human E. coli isolates affects phage susceptibility possibility by downregulating a defense mechanism against invading DNA. Finally, we examined the repartition of phages and bacteria through mucosal and luminal gut sections and observed a heterogeneous spatial distribution of these two antagonist populations, supporting the hypothesis of source-sink dynamics. Altogether our data demonstrates that multiple factors encompassing, spatial distribution, bacterial physiology and defenses against foreign DNA modulate the interactions between bacteria and phages within the gut

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Fernandez, Benoit. "Activité biologique et impact sur le microbiote intestinal des bactéries lactiques bactériocinogènes." Thesis, Université Laval, 2014. http://www.theses.ulaval.ca/2014/30845/30845.pdf.

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Les bactériocines sont des composés de nature protéique dotés d'une activité antimicrobienne dirigée contre des bactéries phylogénétiquement proches de la souche productrice. Récemment, la production de bactériocines a été évoquée comme un mécanisme d'action important impliqué dans l'activité antimicrobienne des probiotiques au niveau gastro-intestinal. Ce projet de recherche avait pour objectif d’évaluer la capacité de certaines bactéries lactiques bactériocinogènes à produire leur bactériocine dans les conditions physiologique et microbiologique du tractus digestif. Trois souches bactériocinogènes, à savoir Lactococcus lactis biovar diacetylactis UL719 (productrice de nisine Z), Pediococcus acidilactici UL5 (productrice de pédiocine PA-1) et L. lactis ATCC 11454 (productrice de nisine A) ont été utilisées comme modèle lors de ces travaux de thèse. Des expériences menées dans le simulateur de tractus digestif TIM-1 ont montré que P. acidilactici avait un taux de survie de 17 % aux stress rencontrés au niveau de l’estomac et de l’intestin grêle. Le transit dans la partie proximale du système digestif a eu peu d’effet sur l’activité inhibitrice de cette souche. Une légère surexpression des gènes de production de la bactériocine a même été observée à la sortie l’iléon. Contrairement à P. acidilactici UL5, L. lactis ATCC 11454 était moins résistante au stress digestif, avec un taux de survie inférieur à 1 %. Par ailleurs, les trois souches bactériocinogènes étudiées se sont révélées capables de croitre et de produire leur bactériocine dans un milieu de culture simulant le milieu colique. Dans le cas de P. acidilactici, nous avons démontré une inhibition significative de Listeria directement corrélée avec la production de pédiocine puisqu’aucune inhibition n’a été observée avec un mutant non producteur. Enfin, nous avons étudié la capacité de la souche P. acidilactici à survivre et à produire sa bactériocine au niveau iléaque de même que l’impact de cette activité inhibitrice sur l’équilibre du microbiote iléaque chez l’humain. Les analyses microbiologiques ont révélé que P. acidilactici survivait au transit bien qu’elle ne soit pas capable d’y croitre, probablement en raison d’un manque de compétitivité vis-à-vis du microbiote. Ces observations expliqueraient la faible activité inhibitrice de P. acidilactici contre L. monocytogenes que nous avons mesuré.
Bacteriocins are proteinaceous compound naturally produced by several bacterial strains with an inhibition activity directed against closely related bacteria. Recently, the production of bacteriocins was proposed as an important mechanism of action involved in the antimicrobial activity of probiotics in the gastrointestinal tract. This research aimed to evaluate the ability of some bacteriocin-producing lactic acid bacteria to produce their bacteriocins in the physiological and microbiological conditions of the digestive tract. Three strains, namely L. lactis biovar diacetylactis UL719 (producing nisin Z), P. acidilactici UL5 (producing pediocin PA- 1) and L. lactis ATCC 11454 (producing nisin A) were used as models throughout this thesis. Experiments performed with the TIM-1 digestive tract simulator have shown that P. acidilactici had a survival rate of 17 % in the stomach and small intestine. Passage in the proximal part of the digestive tract had little effect on the inhibitory activity of this strain. A slight over-expression of the genes encoding production of bacteriocin has been observed even at the end of the ileum. Unlike P. acidilactici UL5, L. lactis ATCC 11454 was less resistant to gastrointestinal stress, with a survival rate of less than 1 %. In addition, the three bacteriocin-producing strains considered in this study were proved able to grow and produce their bacteriocins in a culture medium simulating the colonic environment. In the case of P. acidilactici, we demonstrated significant inhibition of Listeria in the colonic medium and that this inhibition was directly correlated with the production of pediocin since no inhibition was observed with a non-producing mutant. Finally, we studied the ability of P. acidilactici to survive and produce its bacteriocin in the ileac conditions and the impact of this inhibitory activity on the balance of ileac microbiota of healthy humans. Microbiological analyzes revealed that P. acidilactici survived throughout the transit although it was not able to grow, probably due to a weak competitivity compared to the ileac microbiota. These observations may explain the low inhibitory activity of P. acidilactici against L. monocytogenes that we measured.

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Birer, Caroline. "Le microbiote bactérien cuticulaire des fourmis de Guyane : pouvoir antibiotique et écologie des communautés." Thesis, Guyane, 2017. http://www.theses.fr/2017YANE0003/document.

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Le microbiote bactérien cuticulaire des fourmis (Hymenoptera : Formicidae) est connu pour avoir un rôle défensif chez ces insectes sociaux, notamment chez les fourmis attines (Formicidae : Attini) grâce l’utilisation de molécules antimicrobiennes produites par des actinobactéries cuticulaires. Dans le cadre de cette thèse, nous avons étudié le microbiote bactérien des fourmis de Guyane en utilisant différentes approches en chimie des produits naturels et en écologie moléculaire. Le premier chapitre décrit l’isolement, l’identification, la culture et l’évaluation biologique de 43 actinobactéries cuticulaires de fourmis de Guyane. Les tests d’antagonismes des souches isolées et l’activité antibiotique des extraits de culture contre des micro-organismes pathogènes humains sont présentés ainsi que l’identification d’un dipeptide cyclique (Cyclo(LPro-LPhe)) antimicrobien qui a été isolé à partir d’une souche proche de Streptomyces thioluteus. Par ailleurs, la mise en œuvre de réseaux moléculaires appliqués à une analyse par UPLC/MS/MS de cocultures d’actinobactéries a permis d’explorer la diversité des métabolites produits dans ces conditions. Le deuxième chapitre présente une étude méthodologique pour comparer quatre méthodes d’extraction d’ADN, en termes de richesse et de composition du microbiote bactérien cuticulaire, par séquençage haut débit à partir des espèces Atta cephalotes et Pseudomyrmex penetrator. Les résultats du métabarcoding ADN mettent en lumière deux méthodes d’extraction et révèlent des différences inter- et intraspécifiques dans la composition des communautés bactériennes cuticulaires. Enfin, le chapitre trois décrit la composition du microbiote bactérien cuticulaire des espèces Camponotus femoratus et Crematogaster levior dans les jardins de fourmis. Les résultats soulignent l’acquisition d’une partie du microbiote dans l’environnement. En parallèle l’analyse métabolomique des cuticules montre à contrario une plus grande spécificité liée à l’espèce de fourmi. Les recherches futures axées sur les stratégies d’analyses statistiques combinant le métabarcoding et la métabolomique sont discutées
The bacterial microbiota of ants (Hymenoptera: Formicidae) is known to have a defensive role in social insects, particularly for leaf-cutting ants (Formicidae: Attini) due to the use of antimicrobial molecules produced by cuticular actinobacteria. In this thesis, we studied the bacterial microbiota of ants in French Guyana using different approaches based on natural products chemistry and molecular ecology. The first chapter describes the isolation, identification, culture and biological evaluations of 43 cuticular actinobacteria. Antagonism bioassays of isolated strains and antibiotic activities of the culture extracts against human pathogens are presented as well as the identification of an antimicrobial cyclic dipeptide (Cyclo (LPro-LPhe)) isolated from a strain close to Streptomyces thioluteus. Moreover, the implementation of molecular networks applied to UPLC/MS/MS analysis of actinobacterial cocultures allowed us to explore the diversity of metabolites produced under these conditions. The second chapter presents a methodological study to evaluate the capacity of four DNA extraction methods, in terms of richness and composition of the cuticular bacterial microbiota, in high-throughput sequencing from Atta cephalotes and Pseudomyrmex penetrator. The results of metabarcoding highlight two methods of extraction and reveal inter- and intraspecific differences in the composition of cuticular bacterial communities. Finally, chapter three describes the composition of the cuticular bacterial microbiota of Camponotus femoratus and Crematogaster levior in ant garden and the results reveal the acquisition in the environment of a part of the microbiota. In parallel, metabolomic analyses of ant’s cuticle show, on the contrary, a greater specificity related to the ant species. Future researches focusing on statistical analysis strategies combining metabarcoding and metabolomics data are discussed

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Renoud, Sébastien. "Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : impact sur des communautés fonctionnelles du microbiote racinaire." Thesis, Lyon, 2016. http://www.theses.fr/2016LYSE1143/document.

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Le développement des plantes est conditionné par leurs interactions avec le microbiote racinaire, dont le fonctionnement repose sur des fonctions élémentaires partagées par plusieurs taxons, au sein de groupes fonctionnels. Certains de ces groupes incluent des PGPR (Plant Growth-Promoting Rhizobacteria), qui stimulent la croissance des plantes grâce à différentes fonctions phytobénéfiques. L'inoculation d'une PGPR peut avoir un impact sur la physiologie de la plante et sur les autres partenaires microbiens de la racine. D'ailleurs, une PGPR inoculée peut modifier la structure génétique du microbiote racinaire global, sans que l'on sache comment cet impact se concrétise au niveau de groupes fonctionnels particuliers. L'hypothèse de cette thèse est que les PGPR inoculées peuvent modifier la structure de communautés microbiennes fonctionnelles importantes pour le développement de la plante. Ces travaux ont évalué l'impact de l'inoculation de la PGPR Azospirillum lipoferum CRT1 sur la taille et/ou la diversité des diazotrophes, des producteurs d'1-aminocyclopropane-1-carboxylate (ACC) désaminase et des producteurs de 2,4-diacétylphloroglucinol (ainsi que de la communauté bactérienne totale) dans la rhizosphère du maïs cultivé en champ sous différents intrants azotés. Nos travaux ont montré que diazotrophes et producteurs d'ACC désaminase pouvaient être co-sélectionnés dans la rhizosphère du maïs, et que l'inoculation modifiait la composition taxonomique de ces groupes fonctionnels. En conclusion, l'inoculation de PGPR module la sélection rhizosphérique de taxons telluriques portant des fonctions phytobénéfiques, ce qui pourrait contribuer aux effets phytobénéfiques observés
Plant development is influenced by interactions established with root microbiota. Microbiota functioning relies on individual functions carried out by functional groups, which often contain multiple microbial taxa. Some of these groups include plant growth-promoting rhizobacteria (PGPR), which stimulate plant growth thanks to several plant-beneficial functions. PGPR inoculation may impact plant physiology and microbial partners of roots, and inoculated PGPR can modify the genetic structure of the root microbiota. However, it is not known how this impact materializes at the level of particular microbial functional groups. The hypothesis of this thesis is that inoculated PGPR will also modify the structure/composition of microbial functional groups important for plant development. This work assessed the impact of inoculation with the PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of diazotrophs, 1-aminocyclopropane-1-carboxylate (ACC) deaminase producers and 2,4-diacetylphloroglucinol producers (as well as the total bacterial community) colonizing the maize rhizosphere in three fields and under different nitrogen fertilization regimes. Our work showed that diazotrophs and ACC deaminase producers could be co-selected in maize rhizosphere and that PGPR inoculation modified the taxonomic composition of functional groups. To conclude, PGPR inoculation modulates rhizospheric selection of microbial members of functional groups important for plant growth, which may mediate some of the plant-beneficial effects of PGPR inoculants

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Lopez, Maryeimy Varon. "Descrição da microbiota relacionada às transformações do enxofre em sedimentos de manguezais." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-30102013-144329/.

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Os manguezais são ambientes de transição entre os ecossistemas terrestres e marinhos, essenciais para o crescimento e o desenvolvimento de muitas espécies de elevado interesse ecológico e econômico. Apesar de ter sua importância reconhecida, são constantemente impactados por diversos poluentes que influenciam sua estabilidade. Estes ecossistemas caracterizam-se por serem anaeróbicos, ricos em sulfato e em matéria orgânica, sendo os microrganismos fundamentais na ciclagem de nutrientes, em especial os envolvidos no ciclo do enxofre, onde os procariotos redutores de sulfato (sulphate-reducing prokaryotes, SRP) aparecem como um grupo frequente e com um papel preponderante. O presente estudo mostrou que as comunidades de arquéias, bactérias e bactérias redutoras de sulfato (sulphatereducing bacteria SRB) são abundantes, diversas e responsivas aos estados de intervenção dos manguezais. A abundância medida por qPCR mostrou que as quantidades de arquéias e bactérias aumentam com a contaminação. A diversidade estudada por pirosequenciamento do gene ribossomal 16S DNAr indicou que estes grupos são diversos, mostrando filos Euryarcheota e Crenarcheota do domínio Archaea, e os filos Deltaproteobacteria e Gammaproteobacteria, do domínio Bacteria, como grupos frequentes. A estrutura destas comunidades, avaliada por análises de co-ocorrência, revelou que a microbiota responde à contaminação, diminuindo e simplificando as interações, quanto maior for a contaminação. A diversidade dos grupos relacionados ao ciclo do enxofre, estudada por DGGE (aprA e dsrB), pirosequenciamento (dsrB) e GeoChip (aprA, dsrB), mostrou que a classe Deltaproteobacteria, representada pelas ordens Desulfobacterales e Desulfovibrionales, é o grupo prevalente na redução do sulfato, e as classes Gammaproteobacteria e Betaproteobacteria devem atuar na oxidação do enxofre (sulphur-oxidising - SOB). O GeoChip (aprA, dsrB) foi a única metodologia que permitiu detectar arquéias redutoras de sulfato (gêneros Archaeoglobus e Pyrobaculum), sendo esta a primeira descrição de tais organismos em ecossistemas de manguezais. Desse modo, estes resultados evidenciam que a microbiota em áreas de manguezais responde à contaminação, tendo uma alta frequência de SRB e SOB, ressaltando, assim, a importância do ciclo do enxofre em ambientes de manguezais.
Mangroves are transitional environments between terrestrial and marine ecosystems, essential for the growth and development of many species with high ecological and economical interests. Despite its recognized importance, mangroves are constantly impacted by various pollutants, affecting its stability. These ecosystems are characterized as anaerobic, rich in sulfate and organic matter, where the microorganisms are essential to the nutrient cycling, particularly those involved in the sulfur cycle, where sulphate-reducing prokaryotes (SRP) appear as frequent and taking an important role. The present study showed that communities of archaea, bacteria and sulphate reducing bacteria (SRB) are abundant, diverse and responsive to state intervention of the mangrove. The abundance measured by qPCR showed that the quantities of archaea and bacteria increase with the contamination. The diversity studied by pyrosequencing of the 16S rDNA ribosomal gene indicated that these groups are diverse, showing Euryarcheota and Crenarcheota phyla of the domain Archaea, and Deltaproteobacteria and Gammaproteobacteria classes of the domain Bacteria, as the most frequent groups. The structure of these communities, as assessed by analysis of network, revealed that the microbiota responds to contamination, reducing and simplifying interactions in the higher contamination. The diversity of groups related with the sulfur cycle studied by DGGE (aprA and dsrB), pyrosequencing (dsrB) and GeoChip (aprA, dsrB) showed that Deltaproteobacteria, represented by orders Desulfobacterales and Desulfovibrionales, is a prevalent group in the sulfate reduction, while Gammaproteobacteria and Betaproteobacteria are frequent in the sulfur oxidation (sulfur-oxidising bacteria - SOB). The GeoChip (aprA, dsrB) was the only method that allowed to detect sulfate-reducing archaea (genera Archaeoglobus and Pyrobaculum), which is the first description of these organism on mangrove ecosystems. Thus, these results show that the microbiota in mangroves areas responds to contamination, having a high frequency of SRB and SOB, thus highlighting the importance of the sulfur cycle in mangrove environments.

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Ramalho-Sanchez, Manuela de Oliveira. "Microbioma de formigas com ênfase em Camponotini (Hymenoptera, Formicidae) /." Rio Claro, 2017. http://hdl.handle.net/11449/151247.

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Título original: Comunidades de bactérias de dois gêneros de formigas Polyrhachis (Spiny ants) e camponotus (Carpenter ants)
Orientador: Odair Correa Bueno
Coorientadora: Corrie Saux Moreau
Banca: Fernando Carlos Pagnocca
Banca: Cíntia Martins Perinotto
Banca: James Montoya Lerme
Banca: Priscila Cintra Socolowski
Resumo: A interação simbiótica tem sido uma das responsáveis pela evolução e a biodiversidade de espécies existentes no planeta. Mais estudos abordando diferentes hospedeiros mostram-se necessários para aumentar o conhecimento do significado evolutivo desta associação na natureza. As formigas pertencentes aos gêneros Polyrhachis e Camponotus estão contidas na tribo Camponotini e são estreitamente relacionadas além de possuírem ampla distribuição, hábitos diversificados, e estão frequentemente associadas à endossimbiontes. Entretanto existem poucos estudos nesta área, permanecendo então muitas questões a respeito destas associações. Desta maneira, por meio da técnica de Sequenciamento de Nova Geração (NGS) Illumina MiSeq2000, o presente estudo teve como objetivo: I. explorar a comunidade microbiana de diversas espécies de Polyrhachis distribuídas em toda sua extensão e verificar os fatores que a influenciam. II. caracterizar a comunidade bacteriana associada aos gêneros Colobopsis e Camponotus, e analisar se há diferenças na composição da comunidade bacteriana quando comparada entre os diferentes gêneros, colônias e em todos os estágios de desenvolvimento; III. averiguar como se dá a distribuição da comunidade bacteriana nas diferentes partes do corpo (cabeça, mesossoma e gáster) de Camponotus, e se esta diversidade está associada ao ambiente onde estas Camponotus foram coletadas; IV. caracterizar o ovário de Camponotus textor, utilizando técnicas de histologia (HE), documentar a ... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Symbiotic interaction has been one of the factors responsible for the evolution and biodiversity of species on the planet. More studies addressing different hosts are necessary to increase the knowledge of the evolutionary meaning of this association in nature. The ants belonging to the genera Polyrhachis and Camponotus are contained in the Camponotini tribe and they are closely related in addition to having wide distribution, diversified habits, and are often associated with endosymbionts. However, there are few studies in this area, and many questions remain about these associations. In this way, through the New Generation Sequencing technique (NGS) Illumina MiSeq2000, the present study aimed: I. To explore the microbial community of several species of Polyrhachis distributed throughout its range and to verify the factors that influence it. II. Characterize the bacterial community associated with the genus Colobopsis and Camponotus, and analyze if there are differences in the composition of the bacterial community when compared between different genera, colonies and at all stages of development; III. To determine how the distribution of the bacterial community occurs in the different parts of the body (head, mesosome and gaster) of Camponotus, and if this diversity is associated with the environment where these Camponotus were collected; IV. To characterize the ovary of Camponotus textor using histology techniques (HE), to document the location of Blochmannia and Wolbachia in oogenesis by fluorescence in situ hybridization (FISH), and to suggest the mechanism of development that these bacteria use to reach the egg . These studies have demonstrated that there are several factors that can influence the ant-associated bacterial community, such as host phylogeny, genera, colony, ontogeny, different body parts, and the environment the ant was ... (Complete abstract click electronic access below)
Doutor

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Biaggini, Kelly. "Etude du dialogue système entéro-endocrinien/microbiote intestinal." Rouen, 2015. http://www.theses.fr/2015ROUES035.

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La lumière intestinale héberge 10 puissance 14 bactéries qui sont en contact permanent avec le système entéro-endocrinien et les médiateurs qu’il délivre. L’impact de ces facteurs eucaryotes sur les bactéries de l’intestin n’est pas bien connu. Nous avons donc recherché si Pseudomonas fluorescens était capable ou non de percevoir certains facteurs entéro-endocriniens et si ceux-ci avaient un impact sur la croissance et la virulence de cette bactérie. Les résultats ont montré que ces substances entrainent une modulation de la virulence bactérienne, dépendante du facteur entéro-endocrinien considéré et de l’origine de la souche testée (clinique ou environnementale). Ensuite nous avons montré que l’épinéphrine module le pouvoir cytotoxique et l’adhésion de Pseudomonas aeruginosa PAO1 et Enterococcus faecalis V583 sur cellules intestinales Caco-2/TC7. Ce neurotransmetteur agit donc à la fois sur des bactéries à Gram négatif et positif. Nous avons aussi mis en évidence que la substance P entraine, de manière intéressante, une augmentation de la pathogénicité d’E. Faecalis V583. Dans le but d’apprécier l’effet global de perturbations hormonales sur le microbiote intestinal, la composition bactérienne des contenus caecaux de souris modèle d’anorexie (ABA), a été comparé à celle de souris contrôle et de souris soumises à une restriction alimentaire (RA). Chez les souris ABA, nous avons mis en évidence la présence ou l’absence de certains genres bactériens, comme par exemple Psychrobacillus. L’ensemble de ce travail montre que certaines bactéries intestinales perçoivent les facteurs entéro-endocriniens et que ceux-ci modulent la virulence bactérienne alors que dans le cas de pathologies aussi variées que la maladie de Crohn ou l’anorexie, des déséquilibres hormonaux sont constatés. Cette thèse ouvre donc de nouvelles perspectives pour une meilleure compréhension des pathologies liées à l’axe intestin/cerveau
The human gastrointestinal tract is colonized by approximatively 10 to the power of 14 bacteria which are in contact with the entero-endocrine system and its hormonal mediators. The influence of these eukaryotic factors on the gut microbiota is not very well known. Therefore, in the present work, we investigated the effect of several entero-endocrine factors on the growth and virulence of P. Fluorescens. Interestingly the results showed that entero-endocrine factors can led to a modulation of bacterial virulence depending on the eukaryotic substances tested and the origin of bacterial strain (clinical or environmental). In further work, we decided to study the impact of epinephrine on two opportunistic pathogens: Pseudomonas aeruginosa PAO1 and Enterococcus faecalis V583. We showed that epinephrine can modulate the cytotoxic potential and adhesion of these bacteria on Caco-2/TC7 cells. We thus conclude that this neurotransmitter is able to act on both Gram negative and Gram positive bacteria. Our work suggests that P. Aeruginosa and E. Faecalis could have sensors to epinephrine even if their nature still has to be determinated. In our study, we could highlight that Substance P enhances the pathogenicity of E. Faecalis V583. To evaluate the global effect of hormonal imbalances on the composition of intestinal microbiota, caecal contents of activity-Based anorexia (ABA) mice were compared to control and limited food access (LFA) mice. We observed that several bacterial genera appeared or disappeared among the gut microbiota of ABA mice, such as Psychrobacillus. Taken together, our study demonstrates that intestinal factors may be sensed by the gut microbiota and could probably participate in health and disease. Entero-endocrine factors can modulate bacterial virulence while precisely hormonal imbalances are noticed in pathologies such as Crohn disease or anorexia. This work opens new perspectives for a better understanding of diseases linked to the gut/brain axis

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Potiron, Aline. "Conversion du cholestérol en coprostanol par les bactéries du microbiote intestinal humain et impact sur la cholestérolémie." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLA036/document.

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La réduction du taux de cholestérol (CH) sanguin est un point clé dans la lutte contre les maladies cardiovasculaires. L’efficacité contrastée des médicaments disponibles actuellement ainsi que l’intérêt porté autour du microbiote intestinal dans la régulation de la physiologie de l’hôte nous amènent à envisager cette voie comme alternative thérapeutique. La production de coprostanol (CO), dérivé très peu absorbé du CH, par des bactéries de ce microbiote a été corrélée positivement à une faible cholestérolémie. Les objectifs de cette thèse sont i) d’isoler et d’identifier de nouvelles souches bactériennes ayant cette activité, ii) d’identifier les gènes bactériens responsables de cette transformation et iii) de détereminer l’impact de ce métabolisme sur la physiologie de l’hôte. Nous avons isolé 22 nouvelles souches productrices de CO à partir des selles d’un individu en produisant beaucoup. Nous avons choisi les souches Bacteroides sp. D8 et Bacteroides sp. BV pour la construction de deux banques génomiques et huit autres pour des essais d’implantation in vivo dans le tractus gastro-intestinal (TGI) de souris axéniques. Nous avons identifié 55 clones potentiellement positifs par le criblage fonctionnel des banques génomiques. Leurs analyses supplémentaires devraient nous apporter des informations sur les gènes impliqués dans cette activité. Toutes les bactéries sélectionnées sont capables de coloniser le TGI de la souris axénique. La souche Parabacteroides distasonis est la meilleure souche productrice de CO in vivo. Nous avons testé son effet sur la cholestéolémie chez des souris axéniques soumises à un régime riche en CH sur 11 semaines en comparaison avec une souche non productrice in vitro, B. dorei, et avec des souris conventionnalisées comme contrôle. La souche B. dorei produit du CO in vivo, soulignant l’importance de l’environnement dans l’activité de production de CO déjà supposée d’après la littérature et nos résultats in vitro. Des gènes impliqués dans l’excrétion du CH de l’organisme vers les selles sont surexprimés chez ces souris et celles colonisées avec P. distasonis. Cependant seules ces dernières présentent une cholestérolémie plus faible que les souris conventionnalisées. Le mécanisme impliqué semble indépendant de la production de CO et de l’excrétion de CH car les mêmes quantités de ces composés sont retrouvées dans les selles indépendamment du statut bactérien. Les concentrations en acides biliaires totaux dans la bile et dans les selles sont supérieures pour les souris monocolonisées comparées au conventionnalisées. Les selles des souris colonisées avec P. distasonis présentent plus d’acides urso- et chénodésoxycholiques que les souris conventionnalisées et plus d’acide cholique que les souris colonisées avec B. dorei. En conclusion, nous avons isolé de nouvelles souches et identifier des clones potentiellement positifs. Les études in vivo tendent à montrer que l’activité de production de coprostanol n’a pas d’effet sur la cholestérolémie. En revanche, la souche P. distasonis semble diminuer la cholestérolémie par un mécanisme encore inconnu
Cholesterol (CH) level management is a keystone to limit cardiovascular diseases. The contrasted efficiency of the drugs currently available as well as the interest around the intestinal microbiota in regulating the host physiology lead us to consider this pathway as a therapeutic alternative. The production of coprostanol (CO), a very poorly absorbed CH derivative, by bacteria of this microbiota has been positively correlated with low CH plasma level. The aims of this thesis are (i) isolate and identify new bacterial strains possessing this activity, (ii) identify the bacterial genes responsible for this transformation and (iii) determine the impact of this metabolism on host physiology. We isolated 22 new strains producing CO from the stools of a high-coprostanol producing individual. We chose Bacteroides sp. D8 and Bacteroides sp. BV for the construction of two genomic libraries and eight others for in vivo implantation tests in the gastrointestinal tract (GIT) of germ-free mice. We identified 55 potentially positive clones by functional screening of these genomic libraries. Their additional analyzes should provide us with information about the genes involved in this activity. All selected bacteria are capable of colonizing the GIT of germ-free mice. Parabacteroides distasonis is the best strain producing CO in vivo. We tested its effect on blood cholesterol level in germ-free mice subjected to an 11-week CH-rich diet compared to an in vitro non-producing strain, B. dorei, and with conventionalized mice as control. The B. dorei strain produces CO in vivo, emphasizing the importance of the environment in the CO production activity already assumed from the literature and our results in vitro. Genes involved in the excretion of CH from body to feces are overexpressed in these mice and those colonized with P. distasonis. However, only the latter have lower cholesterolemia than conventional mice. The mechanism involved appears to be independent of CO production and CH excretion because the same amounts of these compounds are found in feces independently of bacterial status. Total biliary acids concentrations in bile and feces are higher for monocolonized mice compared to conventionalized mice. The feces of mice colonized with P. distasonis exhibited more urso- and chenodeoxycholic acids than conventionalized mice and more cholic acid than mice colonized with B. dorei. In conclusion, we have isolated new strains and identified potentially positive clones. In vivo studies tend to show that coprostanol production activity has no effect on plasma cholesterol. In contrast, P. distasonis seems to decrease plasma cholesterol by a still unknown mechanism

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Picard, Marion. "Étude de l'implication d’une voie MyD88/IL-22 dans le contrôle de la colonisation par la bactérie segmentée filamenteuse." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCB107/document.

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L’intestin des mammifères est colonisé par une dense communauté microbienne avec lequel il a établi, au cours d’une longue co-évolution, des relations mutualistes. Ces relations, bien qu’essentiellement basées sur des avantages métaboliques permettent également la maturation complète du système immunitaire, dont le développement est initié in utero par un programme génétique. Chez la souris, seule la SFB a été décrite comme présentant un fort pouvoir immunostimulant permettant la coordination d’un large panel de réponses immunes, notamment IgA et Th17 dont le site d’induction préférentiel serait les plaques de Peyer. La première partie de ma thèse a contribué à la finalisation de travaux consacrés à l’étude des caractéristiques des réponses IgA et Th17 induites par SFB. Nous avons ainsi mis en évidence la capacité de la SFB à stimuler la maturation post-natale de follicules lymphoïdes isolés et de tissus lymphoïdes tertiaires qui se substitueraient aux plaques de Peyer en tant que sites inducteurs des réponses IgA et Th17 stimulées par SFB. Cependant, ce microbiote constitue aussi une source antigénique importante pouvant représenter une menace pour l’intégrité de l’hôte. Notamment, la SFB peut provoquer une inflammation chronique délétère en périphérie de l’intestin, chez des souris prédisposées génétiquement. Cela suggère l’existence de mécanismes capables de réguler la colonisation par la SFB, afin d’éviter tout phénomènes compromettant l’intégrité physiologique de l’hôte. À l’aide de souris immunodéficientes axéniques ou seulement colonisées par SFB, nous avons pu mettre en évidence un rôle de la voie de signalisation des TLR dans le contrôle de la colonisation par SFB. Cependant, ni les peptides anti-microbiens, ni les IgA ne semblent impliqué dans le contrôle de la colonisation par SFB
The mammalian intestine is heavily colonized by a huge microbial community. During a long coevolution process, the host has evolved mutualistic relationships with its microbiota. Thes relationships, mainly based on metabolstic advantages, also allow the full maturation of the host immune system, which development is initiated in utero by a genetic program. In mice, only SFB has been yet described to display strong immunostimulant properties allowing the coordination of a large panel of immune responses, more specifically IgA and Th17 responses, which preferential induction sites might be the Peyer's patches. The first part of my thesis contributed to complete a work dedicated to the characterization of the IgA et Th17 responses induced by SFB. We have underscored SFB capacity to stimulate the post-natal maturation of isolated lymphoid follicles and also tertiary lymphoid tissues that would substitute to Peyer's patches as inductors sites of both IgA and Th17 responses induced by SFB. However, this microbiote also constitutes a potential antigenic threat for the host integrity. Notably, the SFB could provoke chronic deleterious inflammation in peripheric compartment in genetically predisposed individuals. It suggests the establishment of highly regulated mechanisms regulating SFB colonization, to avoid compromising events for the host homeostasis. In a second part of my thesis, with the help of immunodeficient axenic mice, we have shown a role of TLR signaling pathways in the control of SFB colonization. However, antimicrobial peptides, IgA, IL-17 or IL-22 seem to be involved int eh control of SFB colonization

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Benjdia, Alhosna. "Maturation des sulfatases chez les procaryotes : caractérisation d'une enzyme de la famille des SAM radical et étude de son rôle dans le dialogue bactéries-hôte." Paris 11, 2008. http://www.theses.fr/2008PA112312.

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Les sulfatases sont des enzymes bactériennes largement distribuées des eucaryotes aux procaryotes. Une des particularités des sulfatases est qu’elles doivent subir une modification post-traductionnelle au niveau de leur site actif pour être fonctionnelles. Cette modification consiste en une oxydation d’un résidu de cystéine ou de sérine qui aboutit à la formation d’un acide aminé modifié, la Calpha-formylglycine. Ce résidu est présent au sein d’un motif particulier défini par la séquence : C/SxPxR. Ce motif n’est pas exhaustif puisque nous avons identifié chez C. Perfringens une sulfatase ayant le motif CxAxR. Nous avons également identifié l’enzyme responsable de cette modification que nous avons nommée anSME pour « anaerobic Sulfatase Maturating Enzyme ». La caractérisation biochimique et spectroscopique de cette famille d’enzymes nous a permis de démontrer que les anSMEs appartiennent à la superfamille des enzymes SAM radical. Nous avons également pu établir les premières étapes du mécanisme des anSMEs et démontrer que le radical Ado°, formé suite au clivage de la SAM, à pour cible un proton situé sur le carbone beta du résidu à modifier (i. E. Cystéinyle ou séryle). Parallèlement, nous avons cherché à comprendre le rôle des sulfatases dans les intéractions eucaryotes-procaryotes via les anSMEs. Pour cela, nous avons réalisé un mutant du gène anSME chez Bacteroides thetaiotaomicron (BT), une bactérie commensale majeure du tube digestif. Nous avons pu montrer que cette fonction est importante au maintien de BT dans le tractus digestif
Sulfatases are widespread enzymes found from eukaryotes to prokaryotes. This class of hydrolases is unique in requiring an essential post-translational modification of a critical active-site cysteinyl or seryl residue to Calpha-formylglycine (FGly). This conversion depends on a strictly conserved sequence called “sulfatase signature”: C/SxPxR. We have isolated from C. Perfringens a sulfatase enzyme with a new motif containing an alanine instead of the conserved proline residue. Nevertheless, the critical residue of this sulfatase is also converted into FGly. Our work has also established that this modification is catalyzed by a new enzyme called “anaerobic Sulfatase Maturating Enzyme” (anSME). The spectroscopic and biochemical characterizations of anSME have demonstrated that this enzyme possesses a [4Fe-4S]2+,+ center which interacts with S-adenoysl-L-methionine to produce 5’-deoxyadenosine (AdoH). AnSMEs thus belong to the so-called radical SAM superfamily. Furthemore, mechanistic investigations have established that anSMEs are dual substrate enzymes able to catalyze both the oxidation of cysteinyl and seryl residue. We have also demonstrated that these enzymes abstract a protium on the beta-carbon atom of the critical residue. In order to investigate the role of sulfatases in host-bacteria relationships, we inactivated the anSME gene in Bacteroides thetaiotaomicron. In presence of the wild type strain, the mutated strain exhibited a fitness defect during the colonization of the digestive tract. AnSME is thus one of the first enzyme involved in commensal bacteria-host relationships

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Beaumont, Martin. "Effets des régimes hyperprotéiques et des métabolites bactériens dérivés des acides aminés sur la muqueuse du gros intestin." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLA011/document.

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Résumé : Les régimes hyperprotéiques sont couramment consommés mais les conséquences au niveau du gros intestin sont peu connues. L’objectif de la thèse était d’étudier les effets des régimes hyperprotéiques et des métabolites bactériens dérivés des acides aminés sur la muqueuse du gros intestinUne série d’expérimentations animales et in vitro a permis de montrer que deux métabolites bactériens dérivés des acides aminés (le sulfure d’hydrogène et le p-cresol) sont toxiques pour l’épithélium lorsqu’ils sont présents en concentration élevée. Les résultats obtenus lors d’une étude clinique montrent que la quantité et la qualité des protéines alimentaires n’ont pas d’effets marqués sur la composition du microbiote fécal mais modifient les concentrations fécales et urinaires en métabolites bactériens.Ces modifications de l’environnement luminal du gros intestin n’étaient pas associées à une augmentation de la cytotoxicité des eaux fécales in vitro. Néanmoins, dans la muqueuse rectale, l’augmentation de l’apport en protéines a régulé l’expression de gènes impliqués dans le maintien de l’homéostasie et ces effets étaient distincts en fonction de la source de protéines utilisée. Toutefois, le niveau d’apport en protéines n’avait pas d’effet sur les paramètres inflammatoires et histologiques dans la muqueuse. Ces résultats ont été complétés par une étude chez le rat montrant qu’un régime hyperprotéique modifie le transcriptome dans les colonocytes mais n’a pas d’effets délétères en termes d’intégrité de l’ADN, de renouvellement de l’épithélium et de fonction barrière
Abstract: High-protein diets are frequently consumed but the consequences for the large intestine are not well described. The objective of this thesis was to evaluate the effects of high-protein diets and of amino-acid derived bacterial metabolites on the large intestine mucosa. Animal and in vitro studies showed that two amino acid derived bacterial metabolites (hydrogen sulfide and p-cresol) are toxic for the epithelium when present at high concentration. The results obtained in a clinical trial indicate that quantity and quality of dietary protein do not have major effects on the fecal microbiota composition but modify the fecal and urinary concentration of bacterial metabolites.These changes in luminal environment were not associated with an increase in fecal water cytotoxicity in vitro. Nevertheless, in the rectal mucosa, the increase in protein intake regulated the expression of genes implicated in homeostatic processes and these effects were modulated by the source of protein. However, the level of protein intake had no effect on immune and histological parameters in the mucosa. These results were completed with a study in rats showing a clear transcriptome profile in colonocytes induced by a high-protein diet but that was not associated with detrimental effects in terms of DNA integrity, epithelial renewal and barrier function

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RIBEIRO, Sarana Héren Pereira. "Efeitos isolados de cipermetrina e metomil na microbiota humana." Universidade Federal de Pernambuco, 2016. https://repositorio.ufpe.br/handle/123456789/23475.

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CAPES
O Brasil é o maior consumidor de pesticidas. Cipermetrina é um pesticida no grupo dos piretróides, altamente tóxico (classe II). Metomil é um metilcarbamato, extremamente tóxico (classe I). Ambos são credenciados para uso em várias culturas e diversos resíduos de agrotóxicos têm sido encontrados nos alimentos, dos mais variados tipos, no Brasil. Isto levanta o problema que envolve o consumo desenfreado de pesticidas e seus efeitos sobre a microbiota humana. A colonização adequada da microbiota normal impede o adoecimento do organismo, por diversos mecanismos funcionais e de defesa que dependem da atuação de micro-organismos comensais. O objetivo deste estudo foi avaliar os efeitos isolados da Cipermetrina e Metomil sobre a microbiota humana. Os testes realizaram-se com bactérias e leveduras comensais, utilizando espécies comuns da microbiota humana (Escherichia coli, Staphylococcus aureus, S. epidermidis, Candida albicans, C. krusei, C. tropicalis, C. parapsilosis, C. guilliermond). Para os testes foram usados métodos de microtitulação em caldo Mueller-Hinton (para bactérias) e caldo Saboreaud (para leveduras), conforme norma técnica da ANVISA. Cipermetrina e Metomil provaram ser capazes de destruir esses micro-organismos. A ênfase é sobre cipermetrina, cujas concentrações bactericida (0,03 mg) e fungicida (0,03 mg) ficaram muito próximas à Ingestão Diária Aceitável (IDA) estabelecida pela ANVISA (0,05 mg/ kg peso). Portanto, os níveis de consumo de cipermetrina estabelecidos como ingestão segura podem gerar riscos para a saúde. Não se exclui o risco do Metomil que, com ação microbicida em concentrações maiores, é igualmente comprometedor, porque as doses bactericidas e fungicidas também se aproximaram de sua IDA.
Brazil is the largest consumer of pesticides. Cypermethrin is a pesticide in the highly toxic (Class II) pyro-trophic group. Methomyl is an extremely toxic methylcarbamate (class I). Both are accredited for use in several crops and various agrotoxic residues have been found in foods in Brazil. This raises the problem that involves the uncontrolled consumption of pesticides and their effects on a human microbiota. An adequate colonization of the normal microbiota prevents the organism from becoming diseased, through several functional and defense mechanisms that depend on the performance of commensal microorganisms. The objective of this study was to evaluate the isolated effects of Cypermethrin and Methomyl on a human microbiota. The tests were carried out with bacteria and commensal yeasts, using common species of the human microbiota (E. coli, Staphylococcus aureus, S. epidermidis, Candida albicans, C. krusei, C. tropicalis, C. parapsilosis, C. guilliermond). For the tests, microtiter methods were used in Mueller-Hinton broth (for bacteria) and Saboreaud broth (for yeasts), according to the ANVISA technical standard. Cypermethrin and Metomil proved to be capable of destroying these microorganisms. The emphasis is on cypermethrin, whose bactericidal (0.03 mg) and fungicidal (0.03 mg) were very present in the Acceptable Daily Intake (ADI) established by ANVISA (0.05 mg / kg bw). Therefore, the levels of cypermethrin consumption established as safe intake may lead to health risks. The risk of Metomil, which with the bactericidal and fungicidal doses also approached its ADI, is not excluded.

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Nishisaka, Caroline Sayuri. "Impactos da mudança do uso e cobertura do solo na emissão de óxido nitroso e abundância de bactérias desnitrificantes no solo." Universidade Federal de São Carlos, 2018. https://repositorio.ufscar.br/handle/ufscar/10139.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Agriculture is responsible for 80% of nitrous oxide emissions on earth's atmosphere, the most potential greenhouse gas among the three main gases (CO2, CH4 and N2O). Citriculture and silviculture play an important role on Brazilian economics due to the high demand of orange and wood products for exportation. Thus, in order to get a better understand about the role of those cultures on N2O emission, this research aims to evaluate N2O emissions from Citrus sinensis and Eucalyptus spp. crops, adjacent forests of each agriculture field were used as control. Citrus and eucalyptus sites are located in Sorocaba and Salto de Pirapora municipality, both in the state of Sao Paulo, Brazil. In each agriculture field and adjacent forest, eight static chambers were randomly installed, and gas sample were collected during dry and wet region season. Soil samples were collected in each field of study from five random sampling points, for further physicochemical, molecular analysis and microcosm incubation. Gas samples were collected from microcosm after moisture adjustment in 70% of field capacity. All gas samples were analyzed by gas chromatography technique. The number of copies of genes related to denitrifying process (nirK, nirS e nosZ) was determined by quantitative real time PCR. Seasonality had significant (P<0.05) influence on N2O emission in field, and N2O fluxes in incubated soil. It was observed positive correlation among dissolved organic carbon (DOC) concentration on soil, soil and plant residue total carbon and nitrogen content and N2O emissions. High nirK, nirS and nosZ gene abundance was found on soil collected during wet season, comparing to those collected on dry season, in both field and microcosm, which was correlated with DOC content and soil moisture. However, there were not significant differences on genes abundance comparisons between cultivated soils and adjacent forests. In conclusion, the seasonality has influence in both N2O emission and denitrifying bacteria abundance present in citrus- and eucalyptus-cultivated soils, mainly through the effects on soil and plant residue physicochemical characteristics, especially those related to COD and soil moisture.
A agricultura é responsável por 80 % do óxido nitroso (N2O) emitido para a atmosfera terrestre, o qual é considerado, dentre os principais gases causadores do efeito estufa, aquele com maior potencial de aquecimento global. A citricultura e a silvicultura são culturas agrícolas que apresentam importante papel na economia brasileira, devido a alta demanda de exportação de produtos derivados da laranja e da madeira. A fim de entender como essas culturas influenciam na emissão do N2O, esse trabalho teve como objetivo avaliar as emissões de N2O a partir de solos cultivados com Citrus sinensis e Eucalyptus spp. Solos florestais adjacentes às áreas agrícolas foram utilizados como controle. As áreas cultivadas com citros e eucalipto estão localizadas nos municípios de Sorocaba e Salto de Pirapora, respectivamente, ambos no estado de São Paulo, Brasil. Em cada área agrícola e florestal, oito câmaras estáticas foram aleatoriamente instaladas e amostras de gases foram coletadas durante o período seco e úmido. Amostras de solo foram coletadas em cada área de estudo a partir de cinco pontos amostrais, as quais foram submetidas a análises físico-químicas, moleculares e incubação em microcosmo. Amostras de gases também foram coletadas a partir dos ensaios de incubação do solo em microcosmos após ajuste da umidade em 70 % da capacidade de campo. Todas as amostras de gases foram analisadas pela técnica de cromatografia gasosa. O número de cópias de genes relacionados com o processo de desnitrificação (nirK, nirS e nosZ) foi determinado por PCR quantitativo em tempo real. A sazonalidade mostrou efeito significativo (P<0,05) nas emissões de N2O em campo, e nos fluxos de N2O determinados a partir do solo incubado. Foi mostrada correlação positiva entre a concentração de carbono orgânico dissolvido (COD) no solo, o teor de carbono e nitrogênio total em solos e resíduos vegetais e as emissões de N2O. Maior abundância dos genes nirK, nirS e nosZ foi encontrada nas amostras de solo coletadas no período úmido em comparação com aquelas coletadas no período seco, tanto em campo como em microcosmo, a qual foi correlacionada com a concentração de COD e a umidade do solo. Contudo, não houve diferença significativa na abundância de tais genes quando comparadas amostras de solos cultivados e florestais adjacentes. Tomados conjuntamente, os resultados permitiram concluir que a sazonalidade influencia tanto a emissão de N2O quanto a abundância de bactérias desnitrificantes presentes em solos cultivados com citros e eucalipto, mediante, principalmente, os efeitos nas características físicas e químicas do solo e dos resíduos vegetais, especialmente aqueles relacionados com o COD e umidade do solo.
FAPESP: 2016/15289-4
FAPESP: 2017/17441-0

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Lastours, Victoire de. "Impact des fluoroquinolones sur la résistance bactérienne dans les microbiotes humains." Paris 7, 2014. http://www.theses.fr/2014PA077096.

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Les fluoroquinolones (FQ) sont des antibiotiques parmi les plus prescrits au monde. L'augmentation importante des prescriptions de FQ est accompagnée de l'émergence inquiétante de la résistance bactérienne responsable d'échecs cliniques et d'émergence de bactéries multi-résistantes. Les FQ diffusent très bien dans les écosystèmes, expliquant leur impact particulier au niveau des microbiotes. Or, les microbiotes humains constituent un réservoir majeur de la résistance bactérienne. Dans un premier volet épidémiologique, nous avons déterminé la prévalence du portage de résistance aux FQ dans les différents microbiotes de patients hospitalisés ainsi que les taux d'émergence de résistance chez des patients traités par FQ. Nous avons montré que chaque microbiote se comportait de façon indépendante en termes de facteurs de risque de portage de souches résistantes, comme d'émergence de la résistance sous traitement. Dans une seconde partie, nous avons montré dans le microbiote nasal et intestinal, que l'émergence de la résistance aux quinolones était un phénomène fréquent aux dynamiques variables, essentiellement dû à l'acquisition de souches résistantes exogènes. Enfin, nous avons montré que les souches résistantes pouvaient persister dans le tube digestif, parce qu'elles étaient particulièrement bien adaptées au commensalisme, leur conférant un avantage sélectif. Ceci expliquerait les taux importants de colonisation par des souches de Escherichia coli résistantes aux quinolones dans le microbiote intestinal chez l'homme avec la double conséquence d'augmenter les risques de transmission interindividuelle et les risques d'infections par ces souches résistantes
Fluoroquinolones (FQ) are among the most prescribed antibiotics in the vvorld. The significant increase in prescriptions of FQ is accompanied by the alarming emergence of bacterial resistance responsible for clinicat failures and the emergence of mufti- resistant bacteria. FQ diffuse very well in ecosystems, explaining the magnitude of their impact on microbiota. Yet, microbiota are major reservoirs of antibiotic resistance. In a first epidemiological chapter, we determined the prevalence of carriage of FQ resistance in different microbiota of hospitalized patients and the rates of emergence of resistance in microbiotas of patients treated with FQ. We showed that each microbiota behaved independently in terms of risk factors for carriage of resistant strains, as well as in terms of emergence of resistance after treatment. In a second chapter, we showed that in the nasal and intestinal microbiota, the emergence of quinolone resistance was a common phenomenon which dynamics were variable, predominantly the result of acquisition of exogenous resistant strains. Finally, we showed that resistant E. Coli strains could persist in the gut, because they were particularly well adapted to commensalism, conferring them a selective advantage. This probably explains high rates of quinolone-resistant strains found in the intestinal microbiota. These strains seem to be able to persist in the long term with the double effect of increasing the risk of further interindividual transmission and the risk of infections by these resistant strains

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38

Berrou, Kevin. "Développement d’outils innovants pour l'étude de l’infection chronique." Thesis, Nîmes, 2019. http://www.theses.fr/2019NIME0001.

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Un des enjeux majeurs dans la gestion de la plaie de pied diabétique est l’obtention d’informations permettant d’anticiper l’évolution de ces infections. Actuellement, il n’existe pas d’outils suffisamment efficaces qui permettent de distinguer une plaie colonisée d’une plaie infectée. L’approche proposée est basée sur discrimination de plusieurs bactéries fréquemment retrouvées dans les plaies chroniques de pied diabétique à partir de leur profil métabolique, et plus particulièrement des métabolites volatils qu’elles produisent. En effet, le dynamisme du métabolisme bactérien serait à même de mettre en évidence les changements qui s’opèrent dans la plaie. Dans un premier temps, une nouvelle méthodologie de concentration des métabolites volatils par Stir Bar Sorptive Extraction (SBSE) a été développée. Elle est basée sur l’utilisation de barreaux qui sont placés à la fois dans le milieu de culture et en espace de tête, suivie d’une analyse par GC-MS. La méthode a ensuite été comparée avec une autre méthode de concentration utilisant des fibres (la SPME) et a montré une meilleure capacité de concentration, permettant ainsi une détection plus sensible. Cette méthodologie a ensuite été utilisée pour suivre la production métabolique de six souches bactériennes cultivées dans des conditions mimant la plaie chronique. Grâce à leur profil métabolique, il a été possible de distinguer des espèces bactériennes. De plus, de manière plus surprenante, il a été possible de distinguer deux souches de Staphylococcus aureus présentant des profils de virulence différents. Enfin, une étude en co-culture a mis en évidence que 83% des métabolites produit en culture simple étaient retrouvés, prouvant l’intérêt de la méthodologie pour distinguer des souches bactériennes d’une même espèce au sein d’une plaie
One of the major challenges in the management of diabetic foot wounds is to obtain information to anticipate the evolution of these infections. Currently, there are no sufficiently effective tools to distinguish a colonized wound to an infected wound. The proposed approach is based on the discrimination of several bacteria frequently found in chronic diabetic foot wounds from their metabolic profile, and more specifically the volatile metabolites they produce. Indeed, the dynamism of bacterial metabolism would be able to highlight the changes that are occurring in the wound. First, a new methodology for the concentration of volatile metabolites by Stir Bar Sorptive Extraction (SBSE) was developed. It is based on the use of stir bars that are placed both in the culture medium and in headspace, followed by GC-MS analysis. The method was then compared with another concentration method using the fibres (SPME) and we highlighted a better concentration capacity with a more sensitive detection. This methodology was then used to monitor the metabolic production of six bacterial strains grown under conditions mimicking the chronic wound. Their metabolic profile allowed us to distinguish bacterial species. Moreover, more surprisingly, it was possible to distinguish two strains of Staphylococcus aureus with different virulence profiles. Finally, a co-culture was performed and we showed that 83% of the metabolites produced in simple culture were found, proving the interest of the methodology to distinguish bacterial strains of the same species within a wound

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39

Ferreira, Mércia de Freitas [UNESP]. "Bactérias endofíticas em tecidos de cafeeiro sob diferentes concentrações de CO2." Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/151319.

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Os microrganismos endofíticos ocorrem naturalmente em todas as partes do cafeeiro e produzem metabólitos secundários que podem influenciar as características da expressão da bebida, bem como a resistência da planta às doenças e pragas. O aumento da concentração atmosférica de CO2 vem sendo observado nas últimas décadas e pode afetar positiva, negativamente ou ser neutro na planta de café, e também influenciar na comunidade de microrganismos endofíticos. A melhor forma de se realizar os estudos com o aumento da concentração de CO2 é por meio de experimento tipo FACE (Free Air Carbon Dioxide Enrichement), o qual possibilita obter uma resposta sem alterar o microclima em áreas extensas de amostragens. Diante disso, o presente trabalho teve por objetivo estudar a comunidade bacteriana endofítica em folhas, frutos e ramos de cafeeiro da variedade Catuaí Vermelho IAC 144, cultivados no experimento ClimapestFACE da Embrapa Meio Ambiente, bem como identificar as bactérias endofíticas presentes em frutos e ramos de café por meio de sequenciamento em larga escala. O experimento FACE é composto por 12 anéis, dos quais seis com a concentração atual de CO2 que é de aproximadamente 400 ppm e os outros seis enriquecidos com CO2 até uma concentração de 550 ppm. Em cada anel, foram coletados folhas, ramos e frutos nas safras de 2013 a 2015. Com os tecidos amostrados foi realizada análises por meio da técnica de T-RFLP (Restriction Fragment Length Polymorphism), onde na amplificação do gene 16S rDNA de todas as amostras foram utilizados primers específicos para bactérias universais. Para a identificação da comunidade endofítica foi utilizado 16S rDNA de oito amostras de frutos e de três fragmentos de ramos, provenientes de quatro anéis com CO2 ambiente e quatro anéis enriquecido com CO2 de uma mesma planta, dos dois anos de coleta, totalizando 16 amostras selecionadas para o sequenciamento realizado pela técnica Ion Torrent. Os dados da técnica de T-RFLP foram analisados pelo teste ANOSIM e observadas diferenças quando comparados os agrupamentos entre folhas, frutos e ramos, contudo não foram observadas diferenças entre os tratamentos com CO2 ambiente e com enriquecimento de CO2. A Análise de Componentes Principais veio a confirmar o resultado do teste ANOSIM revelando que a estrutura das comunidades bacterianas endofíticas apresentam maior dissimilaridade quando comparadas as partes das plantas (folha, fruto e ramo). Mas ao comparar os tratamentos com CO2 ambiente e com enriquecimento de CO2, houve uma similaridade e em alguns casos havendo sobreposição, o que mostra que não houve distinção das comunidades entre os tratamentos. O sequenciamento em larga escala de amostras de frutos e ramos de cafeeiro revelou que a microbiota endofítica, que habita estes tecidos vegetais, são na sua grande maioria bactérias pertencentes aos filos Proteobactéria, Actinobactéria e Firmicutes. Quando se comparou os tecidos em que estes microrganismos vivem (frutos e ramos), a maior abundância foi encontrada colonizando os tecidos dos ramos. As plantas desenvolvidas na concentração de CO2 ambiente apresentaram maior predominância de bactérias endofíticas que as cultivadas em ambiente enriquecido com CO2.
Endophytic microorganisms occur naturally in coffee plant and produce secondary metabolites that can influence the beverage characteristics, as well as the resistance of plant diseases and pests. The increase in the atmospheric CO2 concentration has been observed in the last decades and can affect positively, negatively or be neutral to coffee plant, and also influence the endophytic microorganisms. The best way to carry out the studies with the increase of CO2 concentration is in FACE experiment (Free Air Carbon Dioxide Enrichement). The objective of this study was to study the endophytic bacterial community in leaves, fruits and branches of coffee grown in the ClimapestFACE experiment at Embrapa Environment, as well as to identify the endophytic bacteria in fruits and branches of through large-scale sequencing. The FACE experiment consists of 12 rings, of which six maintains the ambient CO2 concentration (400 pm) and other six enriched with CO2 at 550 ppm. In each ring were collected leaves, branches and fruit between 2013 and 2015. Samples were analyzed using T-RFLP technique, where specific universal bacteria primers were used in the amplification of 16S rDNA gene. For identification of endophytic community sequencing was performed through Ion Torrent technique. The data of T-RFLP technique were analyzed by ANOSIM test and differences were observed when comparing the groupings between leaves, fruits and branches, however no differences were observed between treatments with or without CO2 enrichment. The Principal Component Analysis confirmed the ANOSIM test and revealed that the structure of endophytic bacterial communities presents greater dissimilarity when comparing leaf, fruit and branch. However, in the comparison between treatments with and without CO2 enrichment there was a similarity and in some cases overlap, which shows that there was no distinction between communities. The largescale sequencing of coffee fruit and branches revealed that endophytic microbiota, which inhabits these plant tissues, are Proteobacteria, Actinobacteria and Firmicutes. When comparing the community of microorganisms in the tissues, the branches present greater abundance than the fruits. Plants developed in the ambient CO2 concentration had a greater predominance of endophytic bacteria than those grown in an environment enriched with CO2.

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40

Biscola, Vanessa. "Interações entre bactérias láticas produtoras de bacteriocinas e a microbiota autóctone de charque." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/9/9131/tde-06062013-154005/.

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O charque é um produto cárneo tipicamente brasileiro, salgado e seco ao sol, ainda produzido de maneira artesanal. Durante sua produção há uma etapa de fermentação, realizada pela microbiota naturalmente presente na matéria-prima, o que dificulta a padronização do produto, e pode influenciar negativamente em suas características sensoriais e qualidade microbiológica. O controle da etapa de fermentação do charque seria uma alternativa para minimizar este problema e, neste contexto, as bactérias láticas produtoras de bacteriocinas se enquadram de forma interessante. A microbiota autóctone de charque inclui principalmente bactérias láticas e micro-organismos halofílicos e halotolerantes, sendo assim, este produto apresenta potencial como fonte para o isolamento de novas bactérias láticas produtoras de bacteriocinas. Assim, este trabalho teve por objetivo isolar e identificar culturas de bactérias láticas produtoras de bacteriocinas naturalmente presentes no charque, caracterizar parcialmente as bacteriocinas produzidas por essas culturas, avaliar seu potencial de aplicação neste produto para a melhoria de sua qualidade microbiológica e avaliar seu efeito na ecologia microbiana do charque, nas diferentes etapas de sua fabricação. Através da técnica de tripla camada em ágar foi isolada uma cepa de Lactococcus lactis subsp. lactis apresentando o gene codificador para nisina Z e com capacidade de inibir, in vitro, micro-organismos medianamente e altamente halotolerantes isolados de charque, além de outros micro-organismos deteriorantes e patogênicos importantes em alimentos, como Lactobacillus spp., Listeria monocytogenes e Staphylococcus aureus. A bacteriocina produzida pela cepa isolada neste estudo também possui características interessantes para sua aplicação na bioconservação de alimentos, como resistencia ao calor, presença de agente químicos e altos teores de NaCl, além de não ser afetada pelo pH. A aplicação dessa cepa em charque modelo resultou na redução de até 2 ciclos log na população de micro-organismos halotolerantes, indicando apresentar um potencial de aplicação como agente de bioconservação do produto. Os ensaios de avaliação da ecologia microbiana, empregando DGGE, indicaram que a fermentação natural do charque ocorreu com a participação de bactérias láticas dos gêneros Lactobacillus, Streptococcus, Lactococcus e de micro-organismos halotolerantes do gênero Staphylococcus. Além disso, os estudos referentes à dinâmica populacional demonstraram que a adição da cepa bacteriocinogênica ao charque não influenciou, de forma qualitativa, as populações presentes no produto.
Charqui is a Brazilian traditional meat product, salted and sun-dried, still manufactured without control of the fermentation step, which is performed by the indigenous microbiota. This fact interferes on the standardization of the product and can negatively affect the sensorial properties and microbiological quality. The application of a known microbiota would be an alternative to minimize this problem and the bacteriocin-producing lactic acid bacteria can can fit in this purpose. The charqui indigenous microbiota mainly includes lactic acid bactéria and halophilic and halotolerant microorganisms, therefore, this product presents a potencial as a source for the isolation of new bacteriocin-producing lactic acid bacteria. The aim of the present work was to isolate and identify bacteriocin-producing lactic acid bacteria from charqui, characterize the bacteriocins produced by the isolated culture, evaluate its potential as biopreservative in charqui and its influence on the microbial populations during the manufacture of the product. A bacteriocinogenic Lactococcus lactis subsp. lactis strain was isolated from charqui through the triple-layer agar technique. This strain produces a nisin-like bacteriocin capable to inhibit in vitro medium and highly halotolerant bacteria isolated from charqui and other food-borne pathogenic and spoilage microorganisms. The application of this strain for charqui manufacturing caused a reduction of up to 2 log in the halotolerant bacteria population, evidencing its potential application for charqui biopreservation. Studies in the populational dynamics using DGGE indicated that the presence of the bacteriocinogenic strain did not affect the microbial populations in the product.

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41

Ferreira, Mércia de Freitas 1980. "Bactérias endofíticas em tecidos de cafeeiro sob diferentes concentrações de CO2 /." Botucatu, 2017. http://hdl.handle.net/11449/151319.

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Orientador: Wagner Bettiol
Coorientador: Rodrigo Mendes
Banca: Kátia de Lima Nechet
Banca: Flávia Rodrigues Alves Patrício
Banca: Adriana Zanin Kronka
Banca: Antonio Carlos Maringoni
Resumo: Os microrganismos endofíticos ocorrem naturalmente em todas as partes do cafeeiro e produzem metabólitos secundários que podem influenciar as características da expressão da bebida, bem como a resistência da planta às doenças e pragas. O aumento da concentração atmosférica de CO2 vem sendo observado nas últimas décadas e pode afetar positiva, negativamente ou ser neutro na planta de café, e também influenciar na comunidade de microrganismos endofíticos. A melhor forma de se realizar os estudos com o aumento da concentração de CO2 é por meio de experimento tipo FACE (Free Air Carbon Dioxide Enrichement), o qual possibilita obter uma resposta sem alterar o microclima em áreas extensas de amostragens. Diante disso, o presente trabalho teve por objetivo estudar a comunidade bacteriana endofítica em folhas, frutos e ramos de cafeeiro da variedade Catuaí Vermelho IAC 144, cultivados no experimento ClimapestFACE da Embrapa Meio Ambiente, bem como identificar as bactérias endofíticas presentes em frutos e ramos de café por meio de sequenciamento em larga escala. O experimento FACE é composto por 12 anéis, dos quais seis com a concentração atual de CO2 que é de aproximadamente 400 ppm e os outros seis enriquecidos com CO2 até uma concentração de 550 ppm. Em cada anel, foram coletados folhas, ramos e frutos nas safras de 2013 a 2015. Com os tecidos amostrados foi realizada análises por meio da técnica de T-RFLP (Restriction Fragment Length Polymorphism), onde na amplificação do gene 16... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Endophytic microorganisms occur naturally in coffee plant and produce secondary metabolites that can influence the beverage characteristics, as well as the resistance of plant diseases and pests. The increase in the atmospheric CO2 concentration has been observed in the last decades and can affect positively, negatively or be neutral to coffee plant, and also influence the endophytic microorganisms. The best way to carry out the studies with the increase of CO2 concentration is in FACE experiment (Free Air Carbon Dioxide Enrichement). The objective of this study was to study the endophytic bacterial community in leaves, fruits and branches of coffee grown in the ClimapestFACE experiment at Embrapa Environment, as well as to identify the endophytic bacteria in fruits and branches of through large-scale sequencing. The FACE experiment consists of 12 rings, of which six maintains the ambient CO2 concentration (400 pm) and other six enriched with CO2 at 550 ppm. In each ring were collected leaves, branches and fruit between 2013 and 2015. Samples were analyzed using T-RFLP technique, where specific universal bacteria primers were used in the amplification of 16S rDNA gene. For identification of endophytic community sequencing was performed through Ion Torrent technique. The data of T-RFLP technique were analyzed by ANOSIM test and differences were observed when comparing the groupings between leaves, fruits and branches, however no differences were observed between treatments with or without CO2 enrichment. The Principal Component Analysis confirmed the ANOSIM test and revealed that the structure of endophytic bacterial communities presents greater dissimilarity when comparing leaf, fruit and branch. However, in the comparison between treatments with and without CO2 enrichment there was a similarity and in some cases overlap, which shows that there was no distinction between communities...
Doutor

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42

Bernard, Lucie. "Utilisation de bactéries du microbiote pulmonaire pour moduler le système immunitaire local à l’état basal et pendant l’infection par Mycobacterium tuberculosis chez la souris." Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30027.

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Les muqueuses du corps humain (notamment l’intestin) sont colonisées dès la naissance par des milliards de microorganismes formant le microbiote (ou flore commensale) et qui vivent en symbiose avec lui. La survie de notre organisme (l’hôte) et de son microbiote dépend de l’état d’activation de notre système immunitaire. Alors qu’une trop faible activation nous rend susceptibles aux infections, une trop forte activation ou inflammation altère nos tissus. Certaines bactéries du microbiote intestinal, interagissent avec les cellules du système immunitaire pour moduler cette balance. Leur administration en tant que probiotique améliore de nombreuses pathologies et est envisagée pour le traitement d’infections respiratoires. L’infection causant le plus de décès dans le monde est la tuberculose, une maladie respiratoire causée par Mycobacterium tuberculosis et dans laquelle une hyper-activation du système immunitaire détruit les tissus pulmonaires. Dans ce projet de thèse, j’ai cherché à savoir si des bactéries du microbiote peuvent influencer la réponse du système immunitaire à la tuberculose, évaluant ainsi le potentiel d’une stratégie probiotique pour améliorer les traitements de cette maladie. En particulier, j’ai fait l’hypothèse que des bactéries commensales isolées du microbiote pulmonaire (récemment décrit) pourraient, par un effet local, fortement modifier cette réponse comme c’est le cas dans l’asthme, chez la souris. Dans un premier temps, j’ai montré que certaines bactéries du microbiote pulmonaire, administrées à des souris saines par voie intranasale, ont une forte capacité à moduler les lymphocytes T CD4+ des poumons tels que les Th1 ou Th17, impliqués dans l’immunité pro-inflammatoire, et les T régulateurs (Treg) réduisant l’activation immunitaire. En particulier, elles induisent la prolifération d’un sous type de Treg exprimant RORt (facteur de transcription caractéristique des Th17), nommé RORt+ Treg, récemment identifié dans l’intestin où l’activation de ces cellules par le microbiote limite les maladies inflammatoires de l’intestin comme la colite. Nous avons montré pour la première fois que ces cellules sont induites dans les poumons de souris traitées avec des bactéries isolées du microbiote pulmonaire appartenant aux genres bactériens Lactobacillus, Staphylococcus et Neisseria et avons caractérisé leur phénotype. Comme dans l’intestin, ces cellules semblent avoir un fort potentiel anti-inflammatoire, soutenu par leur forte expression des molécules inhibitrices CTLA-4, ou PD-1, du marqueur d’activation ICOS et de la cytokine anti-inflammatoire TGF-associée à une faible sécrétion de cytokines pro-inflammatoires telles que le TNF-. De façon intéressante, j’ai observé que des souches de Lactobacillus pulmonaires induisent les mêmes populations leucocytaires dans le modèle murin de tuberculose que dans des souris naïves, et notamment les RORt+ Treg. Tandis qu’aucune des souches testées ne diminuent la charge bactérienne de M. tuberculosis dans les poumons ou la rate des souris infectées, une souche de Lactobacillus murinus (CNCM I-5314) qui augmente fortement les Th17 et les RORt+ Treg, réduit l’infiltration leucocytaire pulmonaire, suggérant sa capacité à réduire l’inflammation associée à cette infection. Bien que la détermination du rôle des Th17 et des RORt+ Treg dans ce phénotype reste à élucider, nos résultats démontrent d’ores et déjà que l’administration de bactéries commensales pulmonaires peut fortement moduler l’immunité locale même au cours d’infections comme la tuberculose. Une meilleure caractérisation des composants du microbiote pulmonaire et des mécanismes par lesquels ils interagissent avec notre système immunitaire pour maintenir la santé respiratoire devrait donc permettre l’émergence d’une nouvelle génération de probiotiques, d’origine pulmonaire, pour prévenir et améliorer le traitement des maladies respiratoires
Human mucosal sites (such as the gut) are colonized from birth by trillions of microorganisms that form the microbiota (or commensal flora), living in symbiosis with our organism. Survival of the host and of its microbiota is dependent on the activation status of our immune system. While poor immune activation results in sensitivity to infections, its uncontrolled activation or inflammation compromises host tissue integrity. Bacteria from the gut microbiota naturally interact with cells of our immune system to preserve an equilibrium. Administration of such commensals as probiotics improve many disease outcomes and is currently studied to improve respiratory infection treatment. The primary infectious cause of death, tuberculosis, a respiratory disease caused by Mycobacterium tuberculosis, involves an over-activation of the immune system causing lung damages. In this thesis project, I investigated whether bacterial strains from the microbiota influence the immune response in tuberculosis to assess the potential of probiotics to improve tuberculosis treatment. In particular, we hypothesized that pulmonary commensal bacteria modify the local immune response to tuberculosis, as recently demonstrated in an asthma murine model. Through intranasal administration in mice, I first identified different lung commensal bacterial strains with a strong ability to modulate the lung CD4+ T cell compartment at steady state. Indeed, these strains induced T-helper (Th) cells involved in pro-inflammatory immunity, such as Th1 and Th17, and regulatory T cells (Treg) involved in anti-inflammatory responses. In particular, they increase proliferation of a specific Treg subtype, expressing RORt (a transcription factor characteristic of Th17). These RORt+ Treg were recently described in the gut, where they are induced by the microbiota and are able to decrease inflammation occurring in the mouse model of colitis. We show for the first time that these cells are induced in the lungs of mice treated with pulmonary bacterial strains from the Lactobacillus, Staphylococcus and Neisseria genera, and characterize their phenotype. As in the gut, these cells seem to have a strong anti-inflammatory profile, supported by their high expression of the inhibitory molecules CTLA-4 and PD-1, activation marker ICOS, and suppressive cytokine TGF- associated to a poor production of pro-inflammatory cytokines such as TNF-. Interestingly, I demonstrate that pulmonary Lactobacillus strains induced the same lung leukocyte populations in the mouse model of M. tuberculosis infection as in naïve mice, including RORt+ Treg. While none of the tested strains reduced M. tuberculosis burden in lung or spleen, the Lactobacillus murinus (CNCM I-5314) strain, which induce a high number of Th17 and RORt+ Treg accompanied by a reduced leukocyte infiltration in the lung, suggesting a capacity to reduce lung inflammation associated with M. tuberculosis infection. The role of Th17 and RORt+ Treg in this phenotype remains to be elucidated. Nevertheless, our results clearly indicate that the administration of pulmonary commensal bacteria strongly modulate the local immunity, even during chronic infections such as tuberculosis. Therefore, a better characterization of the lung microbiota components and of the mechanisms by which they interact with our immune system to maintain health in the respiratory system, might lead to the emergence of a new generation of probiotics, of lung origin, to better prevent and treat pulmonary diseases

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43

Viaud, Sophie. "Etude des effets du cyclophosphamide sur l’immunité anti-tumorale : relations avec le microbiote intestinal." Thesis, Paris 11, 2013. http://www.theses.fr/2013PA11T064.

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Les chimiothérapies conventionnelles anticancéreuses ont été développées dans le but de traiter le cancer par élimination directe et/ou par inhibition de croissance les cellules tumorales en division. Les cellules endothéliales en prolifération à l’origine de la vascularisation intra-tumorale sont également connues pour être sensibles aux effets cytotoxiques des agents anticancéreux. Depuis, de nombreuses études ont montré que certaines thérapies conventionnelles peuvent être exploitées pour leurs capacités anti-angiogéniques (Browder et al. Cancer Research 2000). La stratégie mise en place consiste à suivre des protocoles où la thérapie est administrée à des doses faibles non myéloablatives et plus fréquemment que les thérapies conventionnelles, appelés dosages métronomiques (Hanahan et al. JCI 2000, Gasparini et al. Lancet Oncology 2001). Le cyclophosphamide (CTX) est un agent alkylant communément utilisé en chimiothérapie dans des protocoles à dosage métronomique. Dans les années 1980, 2 études ont montré que le CTX utilisé à dose métronomique pouvait avoir aussi un rôle sur l’immunité en réduisant la fonction suppressive d’une population de lymphocytes T CD4+ dans un modèle expérimental de tumeur (Awwad et al. Cancer Research 1989) et chez des patients atteints de cancer (Berd et al. Cancer Research 1987). Depuis, les connaissances ont progressé et à présent le CTX métronomique est reconnu pour pouvoir limiter l’expansion et les fonctions des lymphocytes T régulateurs (Treg) (Ghiringhelli et al. EJI 2004, Lutsiak et al. Blood 2005) conduisant à une polarisation des cellules T auxiliaires vers un profil Th1 (Matar et al. Eur J cancer 2000 et Cancer Immunol Immunother 2002). Utilisé en association, le CTX métronomique s’avère donc être un outil intéressant dans le traitement anticancéreux (Hermans et al. Cancer Research 2003, Taieb et al. JI 2006). Nos résultats montrent l’importance des lymphocytes T CD4+ sécréteurs d’IL-17 et d’IFNg dans les effets du CTX
Conventional cancer chemotherapies were developed to target cancer cells either by directly eliminating them or by inhibiting the growth of dividing tumor cells. Proliferating endothelial cells at the origin of intratumoral vascularization are known to be sensitive to the cytotoxic effects of antineoplastic agents. Many studies have shown that some conventional therapies can be exploited for their anti-angiogenic capabilities (Browder et al. Cancer Research 2000). The adopted strategy, called metronomic chemotherapy, consists of administering low doses of drug that do not induce myelosuppression, on a more frequent schedule as compared to conventional therapies (Hanahan et al. JCI 2000, Gasparini et al. Lancet Oncology 2001). Cyclophosphamide (CTX) is an alkylating agent commonly used as a metronomic chemotherapy. In the 1980s, two studies demonstrated that when used at a metronomic dosing, CTX could impact the immune response particularly in reducing the suppressive function of a CD4+ T lymphocyte population in an experimental tumour model (Awwad et al. Cancer Research 1989) and in cancer patients (Berd et al. Cancer Research 1987). Since then, knowledge has evolved and now CTX used as a metronomic or low-dose therapy is administered to limit expansion and functions of regulatory T cells (Treg) (Ghiringhelli et al. EJI 2004, Lutsiak et al. Blood 2005), leading to a helper T cell polarization toward a Th1 profile (Matar et al. Eur J cancer 2000 et Cancer Immunol Immunother 2002). When used in combination, CTX turns out to be a potent drug in the antineoplastic treatments armamentarium (Hermans et al. Cancer Research 2003, Taieb et al. JI 2006). Our results demonstrate the importance of CTX effects on IL-17 and IFNg secreting CD4+ T lymphocytes

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Dittmer, Jessica. "Diversity of endosymbiotic bacterial communities in terrestrial isopods : the role of feminizing Wolbachia and other major players." Thesis, Poitiers, 2013. http://www.theses.fr/2013POIT2322/document.

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Les interactions isopodes terrestres-Wolbachia féminisantes constituent un excellent modèle d'étude des interactions multipartites complexes. A ce jour, trois Wolbachia féminisantes, issues d'histoires évolutives différentes, ont été identifiées chez l'hôte Armadillidium vulgare. L'objectif de cette thèse est d'avoir une vue plus complète du microbiote d'A. vulgare et de l'impact des souches de Wolbachia sur cette communauté bactérienne. Dans ce but, des approches quantitative et métagénomique ont été combinées afin de caractériser le microbiote d'A.vulgare à plusieurs niveaux d'intégration: (i) dans des populations naturelles et des lignées contrôlées de laboratoire, (ii) au sein de différents tissus hôtes et (iii) en relation avec le statut d'infection par Wolbachia. Aucun microbiote coeur n'a été mis en évidence malgré une relative homogénéité des communautés symbiotiques dans les tissus de l'hôte. De plus, les bactéries environnementales avaient un impact important sur le microbiote symbiotique. Chez les animaux infectés, Wolbachia représente la bactérie dominante et le facteur majeur de la structuration de la communauté symbiotique. Nous avons également mis en évidence la présence d'un autre constituant majeur du microbiote dans tous les tissus de l'hôte: Candidatus Hepatoplasma crinochetorum, un symbiote facultatif réputé jusque-là pour être seulement associé aux glandes digestives de l'intestin. Afin d'éclairer les interactions potentielles entre hôte et ce symbiote relativement peu connu, la séquence du génome de Ca. H. crinochetorum a été obtenue. Une analyse préliminaire des interactions fonctionnelles des voies métaboliques impliquées dans la digestion de la cellulose nous a permis d'identifier des enzymes cellulolytiques spécifiques de l'hôte et du symbiote. Cette étude ouvre de nouvelles perspectives dans l'étude de la symbiose chez les isopodes
In recent years, there has been a shift of focus in symbiosis studies, away from the traditional 'one host-one symbiont' concept towards a more holistic, community-based approach. This concept takes into account that a host is not only associated with one bacterium, but harbours and interacts with a diverse bacterial community, the microbiome. Terrestrial isopods represent an excellent model system for the understanding of complex multipartite symbioses due to their well-characterised association with feminizing Wolbachia bacteria. To date, three different feminizing Wolbachia strains have been identified in Armadillidium vulgare, presumably representing different host-symbiont co-evolutionary histories. The aim of this PhD was to get a more complete picture of the terrestrial isopod microbiome and the role of Wolbachia within the bacterial community. In order to achieve this, quantitative and metagenomic techniques were combined to characterize the microbiome of A. vulgare on multiple levels: (i) Field vs. lab populations, (ii) in different host tissues, and (iii) in relation to Wolbachia infection status, i.e. presence/absence of Wolbachia as well as infection with different Wolbachia strains. Wolbachia represented the predominant member of the bacterial community in infected individuals and was identified as an important factor influencing bacterial community structure. Apart from Wolbachia, we detected a second highly abundant bacterium: Candidatus Hepatoplasma crinochetorum, a facultative symbiont previously reported from the midgut caeca, was for the first time observed in all tested host tissues. The potential interactions of Wolbachia and Ca. H. crinochetorum constitute an interesting example for symbiont-symbiont relationships between two highly abundant members of a diverse bacterial community

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Cuffaro, Bernardo. "Analyse fonctionnelle de bactéries du microbiote intestinal humain et évaluation de leurs propriétés bénéfiques contre l’obésité et l’inflammation intestinale." Thesis, Lille 2, 2021. http://www.theses.fr/2021LIL2S007.

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Des altérations dans la composition du microbiote intestinal jouent un rôle important dans le développement des pathologies chroniques, tels que l'obésité et les maladies inflammatoires de l'intestin (MICI). Cette dysbiose conduit à la perturbation de plusieurs processus biologiques clés connus pour réguler la physiologie de l'hôte, notamment l'intégrité de la barrière intestinale et les réponses immunitaires conduisant à un état pro-inflammatoire. On observe également une altération de la production d'acides gras à chaîne courte (AGCC), importants métabolites bactériens qui régulent le métabolisme de l’hôte en stimulant la sécrétion de peptides endocrines. Les interventions ciblant le microbiote représentent donc des outils intéressants dans la prise en charge de ces maladies chroniques. Les connaissances sur la composition et les fonctions du microbiote intestinal ont élargi la collection de micro-organismes pouvant avoir un rôle sur la santé de l’hôte. Ces micro-organismes sont susceptibles d’être parfaitement adaptés au tractus gastro-intestinal et dialoguer avec l'hôte. Pour ces raisons, leur évaluation en tant que probiotiques de nouvelle génération (NGP) est en pleine effervescence. Nous avons sélectionné des bactéries dominantes du microbiote intestinal et avons évalué leur robustesse aux conditions environnementales telles que la tolérance à l'oxygène et la survie au stress gastrique et observé une capacité variable selon les souches. Nous avons ensuite caractérisé leurs activités bénéfiques potentielles en utilisant différents modèles in vitro. La plupart d'entre elles ont pu induire la libération d’AGCC dans les surnageants de culture, principalement de l'acétate et dans une moindre mesure de propionate ou de butyrate. Parmi les souches criblées, une majorité a pu restaurer la barrière intestinale en utilisant un modèle in vitro de barrière épithéliale intestinale (Caco-2) et plusieurs souches ont montré un profil anti-inflammatoire après stimulation des cellules immunes humaines (PBMC) et / ou étaient de bons inducteurs de GLP-1 après stimulation de la lignée cellulaire endocrine STC-1. Fait intéressant, certaines d'entre elles ont combiné plusieurs propriétés. Nous avons ensuite évalué in vivo les souches les plus prometteuses dans différents modèles murins d'obésité et de colite. Nous avons identifié trois souches présentant des capacités prometteuses contre l'obésité. Nous avons également montré un effet souche-dépendant de l’espèce Parabacteroides distasonis contre la colite et sélectionné trois souches protectrices. Cette étude nous a apporté de plus amples informations sur la fonctionnalité des bactéries commensales ainsi que des pistes cruciales pour sélectionner des probiotiques de nouvelle génération capables de cibler les maladies chroniques inflammatoires telles que l'obésité et ou les MICI
Alterations in the gut microbiota composition are suggested to play a role in the development of chronic diseases, including obesity and inflammatory bowel disease (IBD). This dysbiosis leads to the disruption of several key biological processes known to regulate the host physiology, notably the gut barrier integrity and the immune responses leading to a pro-inflammatory state. There is also an alteration in the production of Short Chain Fatty Acids (SCFA), key bacterial metabolites that regulate host metabolism by stimulating the secretion of endocrine peptides. Microbiota-targeting interventions therefore represent interesting tools in the management of chronic diseases. The knowledge on the composition and functions of the gut microbiota has extended the range of microorganisms with potential health benefits. These microorganisms are likely to be fully adapted to the gastrointestinal tract environment and to have important interactions with the host and for these reasons they are being evaluated as next generation probiotics (NGPs). We selected dominant bacteria from the gut microbiota and we checked their robustness to environmental conditions such as oxygen-tolerance and their capacity to survive to gastric stress and observed a strain-dependent capacity. We further characterized their potential beneficial activities using different in vitro models. Most of them were able to induce the release of SCFA in the culture supernatants, mainly acetate and to a lower extend propionate or butyrate. Among the screened strains, a majority was able to restore the gut barrier in an in vitro gut epithelial (Caco-2) barrier model and several strains exhibited an anti-inflammatory potential after human immune cells (PBMC) stimulation and/or were good inducers of GLP-1 after STC-1 endocrine cell line stimulation. Interestingly some ofthem combined several properties. We then evaluated in vivo the most promising strains in different murine models of diet-induced obesity and colitis. We identified three strains exhibited promising abilities against obesity. We also showed a strain-dependent effect of Parabacteroides distasonis strains against colitis and selected three effective strains. These studies provide us better insights on the functionality of commensal bacteria and crucial clues to select next-generation probiotics able to target inflammatory chronic diseases such as obesity and related disorders or IBD

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Mirande, Caroline. "Dégradation des fibres pariétales et système xylanolytique de Bacteroides xylanisolvens XB1A et Roseburia intestinalis XB6B4, espèces bacteriennes du microbiote intestinal humain." Clermont-Ferrand 2, 2009. http://www.theses.fr/2009CLF22007.

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Chez l'Homme, les parois végétales contenues dans les fibres alimentaires sont dégradées puis fermentées par les bactéries fibrolytiques du côlon. Le xylane étant l'un des principaux polysaccharides constituant ces parois végétales, deux bactéries possédant de fortes activités xylanolytiques, Bacteroides xylanisolvens XB1A T et Roseburia intestinalis XB6B4, ont été caractérisées. Les activités xylanolytiques de ces espèces vis-à-vis de différents substrats riches en xylanes ont été analysées quantitativement et qualitativement. L'équipement enzymatique de ces souches, comparé par zymogramme, révèle un grand nombre de xylanases. Les activités spécifiques des extraits des deux bactéries sont très élevées et sont majoritairement associées aux cellules. Les gènes codant pour les xylanases de ces deux espèces bactériennes et d'une troisième bactérie xylanolytique du côlon, Bacteroides sp. XB12B, ont été identifiés. Ils codent pour des xylanases appartenant aux familles 10 et 43 des glycosyl-hydrolases, et sont modulaires. Les conditions d'expression de certains de ces gènes ont été etudiées par PCR quantitative, et montrent une régulation par le xylane. Des regroupements de gènes pouvant être impliqués dans la dégradation des hémicelluloses ont été trouvés dans le génome de B. Xylanisolvens. Enfin, une xylanase de la famille 10 des glycosyl hydrolases, produite par B. Xylanisolvens, a été caractérisée : le gène codant cette enzyme a été cloné et la xylanase, nommée Xyn10A, produite chez E. Coli. Cette enzyme, qui pourrait être périplasmique chez B. Xylanisolvens dégrade in vitro les xylanes et les xylooligosaccharides, mai aussi très faiblement la CMC

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Brito, Maria Luísa Saragoça Falcão de. "Metagenomic analysis of saliva microbiome in patients with chronic obstructive pulmonary disease." Master's thesis, Universidade de Aveiro, 2018. http://hdl.handle.net/10773/22041.

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Mestrado em Biologia Molecular e Celular
Microbiome is a community of microorganisms living in a particular environment that englobes all microorganisms with their genes and environmental interactions. The human microbiome plays a pivotal role in human physiology and metabolism being associated to development, nutrition, immunity, and resistance to pathogens and has recognized implications for health and disease. Chronic Obstructive Pulmonary Disease (COPD) is a pulmonary disease characterized by persistent and progressive and nonreversible airflow obstruction. The role of bacteria as a potential pathogenic and etiologic factor in COPD has been a topic of debate for many years. It is thought that lung colonization by particular bacterial strains, in patients with COPD, is responsible for the chronic bronchitis phenotype, increased risk of exacerbations, and loss of lung function. Even though saliva is one of the most easily collectable samples, few studies have been conducted to characterize the saliva microbiome in patients with COPD and even fewer to identify biomarkers that might be informative for disease onset and progression. The aim of this study was to implement the methodology to study the saliva microbiome in patients suffering with COPD, to understand the dynamics of saliva microbiome in the setting of an exacerbation and how the microbiome evolve after that. For that a metagenomic approach was carried out, using the sequencing of the 16S rRNA gene, to analyze 17 samples from 7 patients with COPD, collected at 3 different time points, i.e. at exacerbation, 2 weeks after exacerbation, and at clinical full recovery. In this study, we found microbial shifts in the samples collected at different time points. We also detected high sample variability, especially between samples collected from different individuals. These results suggest that saliva might me a good source of biomarkers for COPD management and may represent an improvement to the implementation of personalized medicine in this population. However, more and larger studies must be conducted.
Microbioma é definido como sendo uma comunidade de microrganismos presente num dado ambiente, que engloba todos os microorganismos com seus genes e interações ambientais. O microbioma humano desempenha um papel importante na fisiologia humana e no seu metabolismo, estando associado ao desenvolvimento, nutrição, imunidade e resistência a agentes patogénicos com implicações na saúde e doença. A doença pulmonar obstrutiva crónica (DPOC) é uma doença pulmonar caracterizada por uma obstrução das vias aéreas persistente progressiva e não reversível. O papel das bactérias como potencial fator patogénico e etiológico na DPOC tem sido tema de debate nos últimos anos. Pensa-se que a colonização dos pulmões por determinadas bactérias, em pacientes com DPOC, é responsável pelo aumento do risco de exacerbações e perda de função pulmonar. Embora a saliva seja uma das amostras mais facilmente recolhida, são ainda poucos os estudos para caracterizar o microbioma da saliva em pacientes com DPOC, e ainda menos para identificar nele biomarcadores informativos sobre o diagnóstico e progressão desta doença. O objetivo deste estudo foi implementar a metodologia que permita estudar o microbioma da saliva em pacientes com DPOC, compreender a dinâmica do microbioma da saliva no contexto de uma exacerbação e como o microbioma evolui depois disso. Para isso, utilizou-se uma abordagem metagenómica utilizando a sequenciação do gene 16S rRNA, para analisar 17 amostras de 7 pacientes com DPOC, recolhidas em 3 momentos diferentes, i.e. em exacerbação, 2 semanas após a exacerbação e após recuperação clínica. Neste estudo foram encontradas e serão descritas diferenças na composição microbiana das amostras colhidas em tempos diferentes. Verificou-se também uma grande variabilidade nos resultados, com grandes diferenças entre as amostras colhidas de diferentes pacientes. Estes resultados sugerem que a saliva pode ser uma boa fonte de biomarcadores para a DPOC e poderá representar um avanço para a implementação da medicina personalizada nesta população. No entanto mais estudos com amostras alargadas são ainda necessários. Contudo, mais estudos deverão ser realizados.

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Marchiori, Ana Carolina [UNESP]. "Diversidade e evolução na simbiose entre bactérias e formigas Attini." Universidade Estadual Paulista (UNESP), 2013. http://hdl.handle.net/11449/110397.

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
As formigas da tribo Attini são conhecidas pelo hábito de cultivar fungos mutualistas (Basidiomycota) em uma variedade de materiais coletados para formar o que é chamado de jardim de fungo. Este hábito teve início há cerca de 50 milhões de anos na América do Sul e deu origem a cinco tipos de agricultura, que diferem no tipo de fungo e material coletado. As attíneas utilizam os jardins de fungos como fonte de nutrientes e enzimas, os quais são produzidos não somente pelo fungo mutualista, mas também por outros microrganismos presentes no ninho. Portanto, para as formigas e fungos terem acesso a nutrientes são necessárias associações com outros microrganismos. Estudos das comunidades microbianas associadas às formigas Attini, na maioria das vezes, estão relacionados aos jardins de fungo e objetivam explorar os mecanismos de degradação da biomassa vegetal. Informações sobre a microbiota associada ao corpo das formigas e sua função ainda são insuficientes. As attíneas dependem dos simbiontes para sua nutrição e proteção contra parasitas. Mas alguns desses microrganismos são ameaças às formigas e outros parecem ser apenas comensais. No presente trabalho, as bactérias associadas às formigas Attini Atta laevigata, Trachymyrmex urichi eMycocepurus goeldii foram identificadas por métodos independentes de cultivo e um cenário no qual a evolução das formigas Attini é moldada pela interação com estes microrganismos foi proposto. Além disso, foi desenvolvido um protocolo de lavagem das formigas para eliminar bactérias externas e ser utilizado para amostrar os microrganismos do interior das formigas. Os resultados mostraram diferenças entre as comunidades bacterianas abrigadas pelas formigas Attini estudadas. A discriminação de bactérias internas e externas ao corpo das formigas foi possível devido à padronização e aplicação do protocolo de lavagem desenvolvido. Foi descoberto que nos intestinos da Attini mais basal M. goeldii predomina uma única espécie de Spiroplasma. No entanto, durante a evolução, esta bactéria foi progressivamente substituída por duas espécies de Rhizobiales no intestino da attínea filogeneticamente intermediária T. urichi, e finalmente uma única espécie de Rhizobiales prevaleceu como a espécie bacteriana única nos intestinos da formiga cortadeira mais derivada A. laevigata. As cortadeiras também carregam em suas cutículas, quantidades consideráveis de Acetobacter. Rhizobiales e Acetobacter pertencem a grupos de bactérias fixadoras de nitrogênio. Assim, é concebível que a especialização em mutualistas fixadores de nitrogênio possa ter desempenhado um papel no aumento do tamanho da população e do tamanho do corpo ao longo da evolução das formigas Attini. O aumento da população pode estar associado com o aumento nas taxas de infecção, mas esta tendência foi aparentemente compensada pela alta complexidade social das cortadeiras e pela manutenção de espécies de Burkholderiales e Actinomycetales, encontradas na sua cutícula. Estas bactérias produtoras de antibióticos podem ter assumido o papel protetor que está atribuído a Pseudonocardiaceae nas demais espécies de Attini. Também foi detectada uma associação com espécies de Wolbachia que parecem ser mutualistas e externas ao corpo das attíneas, provavelmente nas cutículas. Esta associação pode ter iniciado na Attini mais basal, se especializado na intermediária, mas foi perdida na mais derivada. As associações mutualistas parecem ser recentes e ter se originado a partir de uma única aquisição das fixadoras de nitrogênio e múltiplas aquisições de bactérias que produzem antibióticos.
Ants of the Attini tribe are known for the habit of cultivating mutualistic fungi (Basidiomycota) on a variety of harvested materials to form what is called the fungus garden. This habit originated approximately 50 million years ago in South America and gave rise to five agricultural systems, which differ in the type of fungus and collected material. Attine ants utilize the fungus garden as a source of nutrients and enzymes, which are not only produced by the mutualistic fungus, but also by other microbes present in the garden. Therefore, for ants and fungi have access to these nutrients associations with other microorganisms became necessary. Studies of microbial community associated with attine ants are mostly related to the fungus gardens and aim to explore the mechanisms of plant biomass degradation. Information on the microbiota associated with the body of ants and its function are still lacking. Attine ants rely on microbial symbionts for nutrition and protection against parasites. On the other hand, some microbes threatens these ants and others appear to be only commensals. In this work, the bacteria associated with the attine ants Atta laevigata, Trachymyrmex urichi and Mycocepurus goeldii were identified by culture-independent methods and a scenario in which the evolution of attine ants is shaped by the interaction with these microorganisms has been proposed. In the present study a washing protocol was also developed to remove external bacteria, and used to sample microorganisms living inside the ants and possibly other insects. The results showed differences between the bacterial communities harbored by the attine ants studied. Discrimination of internal and external ants’ body bacteria was possible due to the standardization and application of the developed washing protocol. It was observed that the intestines of most basal attine M. goeldii are dominated by a single species of Spiroplasma. However, during the attine ants’ evolution, this bacterium was progressively replaced by two Rhizobiales species in the gut of the phylogenetically intermediate T. urichi, and finally a single species of Rhizobiales prevailed as the unique bacterial species in the gut of the most derived leaf-cutter ant A. laevigata. Leaf-cutters also harbor on their cuticles considerable amounts of Acetobacter sp. Both Rhizobiales and Acetobactersp. species are in the group of nitrogen-fixing bacteria. Thus, it is conceivable that specialization in nitrogen-fixing mutualists may have played a role in increasing population and body size during Attini evolution. A larger population is thought to be associated with increases in infection rates, but this tendency was apparently counterbalanced by high social complexity of leaf-cutters and by the maintenance of Burkholderiales and Actinomycetales species, which we only found in the cuticle of ants. These antibiotic-producing bacteria may have assumed the protective role that is currently attributed to Pseudonocardiaceae in the remaining Attini species. We also detected an association with cuticular Wolbachia mutualists, which may have begun in the more primitive Attini, then specialized in the intermediate ones, and finally being lost in the more derived leaf-cutters. Mutualistic associations appear to be recent and originated from a single acquisition of nitrogen-fixing bacteria and multiple acquisitions of antibiotic producing microbes.
FAPESP: 09/09258-5

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49

Marchiori, Ana Carolina. "Diversidade e evolução na simbiose entre bactérias e formigas Attini /." Rio Claro, 2013. http://hdl.handle.net/11449/110397.

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Orientador: Maurício Bacci Júnior
Banca: André Rodrigues
Banca: Henrique Ferreira
Banca: Fernando Dini Andreote
Banca: Richard Ian Samuels
Resumo: As formigas da tribo Attini são conhecidas pelo hábito de cultivar fungos mutualistas (Basidiomycota) em uma variedade de materiais coletados para formar o que é chamado de jardim de fungo. Este hábito teve início há cerca de 50 milhões de anos na América do Sul e deu origem a cinco tipos de agricultura, que diferem no tipo de fungo e material coletado. As attíneas utilizam os jardins de fungos como fonte de nutrientes e enzimas, os quais são produzidos não somente pelo fungo mutualista, mas também por outros microrganismos presentes no ninho. Portanto, para as formigas e fungos terem acesso a nutrientes são necessárias associações com outros microrganismos. Estudos das comunidades microbianas associadas às formigas Attini, na maioria das vezes, estão relacionados aos jardins de fungo e objetivam explorar os mecanismos de degradação da biomassa vegetal. Informações sobre a microbiota associada ao corpo das formigas e sua função ainda são insuficientes. As attíneas dependem dos simbiontes para sua nutrição e proteção contra parasitas. Mas alguns desses microrganismos são ameaças às formigas e outros parecem ser apenas comensais. No presente trabalho, as bactérias associadas às formigas Attini Atta laevigata, Trachymyrmex urichi e Mycocepurus goeldii foram identificadas por métodos independentes de cultivo e um cenário no qual a evolução das formigas Attini é moldada pela interação com estes microrganismos foi proposto. Além disso, foi desenvolvido um protocolo de lavagem das formigas para eliminar bactérias externas e ser utilizado para amostrar os microrganismos do interior das formigas. Os resultados mostraram diferenças entre as comunidades bacterianas abrigadas pelas formigas Attini estudadas. A discriminação de bactérias internas e externas ao corpo das formigas foi possível devido à... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Ants of the Attini tribe are known for the habit of cultivating mutualistic fungi (Basidiomycota) on a variety of harvested materials to form what is called the fungus garden. This habit originated approximately 50 million years ago in South America and gave rise to five agricultural systems, which differ in the type of fungus and collected material. Attine ants utilize the fungus garden as a source of nutrients and enzymes, which are not only produced by the mutualistic fungus, but also by other microbes present in the garden. Therefore, for ants and fungi have access to these nutrients associations with other microorganisms became necessary. Studies of microbial community associated with attine ants are mostly related to the fungus gardens and aim to explore the mechanisms of plant biomass degradation. Information on the microbiota associated with the body of ants and its function are still lacking. Attine ants rely on microbial symbionts for nutrition and protection against parasites. On the other hand, some microbes threatens these ants and others appear to be only commensals. In this work, the bacteria associated with the attine ants Atta laevigata, Trachymyrmex urichi and Mycocepurus goeldii were identified by culture-independent methods and a scenario in which the evolution of attine ants is shaped by the interaction with these microorganisms has been proposed. In the present study a washing protocol was also developed to remove external bacteria, and used to sample microorganisms living inside the ants and possibly other insects. The results showed differences between the bacterial communities harbored by the attine ants studied. Discrimination of internal and external ants' body bacteria was possible due to the standardization and application of the developed washing protocol. It was observed that the... (Complete abstract click electronic access below)
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Oliveira, Gabriel Silva. "Biofilme multiespécie formado pela microbiota contaminante do leite cru." Universidade Federal de Viçosa, 2017. http://www.locus.ufv.br/handle/123456789/21495.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico
A formação de biofilmes nas indústrias de alimentos é caracterizada, inicialmente, pelo acúmulo de materiais orgânicos em superfícies, sobre as quais comunidades bacterianas podem se formar. Estas estruturas tornam as células mais resistentes e de difícil remoção durante o processo de higienização e representam fonte potencial de contaminação dos alimentos. Objetivou-se neste estudo, avaliar a formação de biofilmes multiespécie em cupons de aço inoxidável pela microbiota contaminante do leite cru e analisar sua diversidade. Foram utilizadas duas amostras de leite, um recém-ordenhado e outro granelizado, com contaminação média de 10 4 UFC/mL e 10 6 UFC/mL de aeróbios mesófilos, respectivamente. Cupons de aço inoxidável foram mantidos imersos no leite a 7 + 2 oC e, a cada dois dias, o leite cru foi trocado por outro de mesma procedência. A formação do biofilme foi acompanhada por contagem padrão em placas das células sésseis e por microscopia de epifluorescência ao longo de 10 dias. No décimo dia, os biofilmes foram observados também por microscopia confocal a laser para determinar a estrutura em seu estado hidratado e visualizar a viabilidade celular. Para analisar a diversidade do biofilme multiespécie, foi utilizada a Eletroforese em Gel de Gradiente Desnaturante (DGGE). As bandas de DNA foram obtidas após amplificação do material genético extraído das células do biofilme utilizando oligonucleotídeos universais para o domínio Bacteria. O número de células sésseis no biofilme formado a partir do leite recém-ordenhado alcançou contagem de 10 5 UFC/cm 2 de psicrotróficos no décimo dia, enquanto o biofilme formado na presença do leite granelizado atingiu 10 6 UFC/cm 2 . A partir do 4o dia de incubação foi observado, pela microscopia de epifluorescência, nos cupons imersos no leite granelizado, aglomerados celulares que possivelmente se tratavam de biofilme, enquanto nos cupons imersos no leite recém- ordenhado essas estruturas foram observadas a partir do 8o dia. Nos cupons que ficaram imersos no leite recém-ordenhado não se visualizou biofilme pela microscopia confocal a laser, enquanto que cupons imersos no leite granelizado foram observados biofilmes com espessuras em torno de 18 μm, com células viáveis desde a base até o ápice. Houve similaridade de 85 % entre a comunidade do biofilme formado na presença das amostras de leite utilizadas. Entretanto, no biofilme formado pela microbiota contaminante do leite recém-ordenhado, a diminuição na diversidade foi observada ao longo dos dias 6, 8 e 10 de incubação, enquanto no biofilme formado pela microbiota contaminante do leite granelizado a diversidade aumentou ao longo do tempo de incubação. Pode-se concluir que a microbiota contaminante do leite cru refrigerado pode se aderir nas superfícies de aço inoxidável e formar biofilmes multiespécies e o grau de contaminação influencia no tempo de formação dessas estruturas.
The formation of biofilms in the food industry is characterized initially by the accumulation of organic materials on surfaces on which bacterial communities can form. These structures make the cells more resistant and difficult to remove during the hygiene process and represent a potential source of food contamination. The objective of this study was to evaluate the formation of multispecies biofilms in stainless steel coupons by the contaminating microbiota of raw milk and to analyze its diversity. It used two milk samples, one freshly milked and the other bulk tanks, with a mean contamination of 10 4 CFU/mL and 10 6 CFU/mL of mesophilic aerobes, respectively. Stainless steel coupons were kept immersed in the milk at 7 ± 2 oC and, every two days, raw milk was exchanged for another of the same origin. Biofilm formation was monitored by standard counting on sessile cells and by epifluorescence microscopy over 10 days. On the tenth day, biofilms were also observed by laser confocal microscopy to determine the structure in its hydrated state and visualize cell viability. In order to analyze the diversity of the multispecies biofilm, Denaturing Gradient Gel Electrophoresis (DGGE) was used. The DNA bands were obtained after amplification of the genetic material, extracted from the biofilm cells and using universal oligonucleotides for the Bacteria domain. The number of sessile cells in the biofilm formed from the freshly milked milk reached a count of 10 5 CFU/cm 2 of psychrotrophs on the tenth day, while the biofilm formed in the presence of the bulk tanks milk reached 10 6 CFU/cm 2 . From the 4 th day of incubation was observed by epifluorescence microscopy, in the coupons immersed in the bulk tanks milk, cell agglomerates that were possibly biofilms, while in the coupons immersed in the freshly milked milk these structures were observed from the 8 th day. In the coupons that were immersed in the freshly milked milk, no biofilm was visualized by laser confocal microscopy, while coupons immersed in the bulk tanks milk were observed biofilms with thicknesses around 18 μm, with viable cells from the base to the apex. There was a similarity de 85% between the community of the biofilm formed in the presence of the milk samples used. However, in the biofilm formed by the contaminating microbiota of freshly milked milk, a decrease in diversity was observed throughout days 6, 8 and 10 of incubation, while in the biofilm formed by the contaminating microbiota of bulk tanks milk the diversity increased over the time of incubation. It can be concluded that the contaminating microbiota of the refrigerated raw milk can adhere to the stainless steel surfaces and form multispecies biofilms and the degree of contamination influences the formation time of these structures.
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