Tesis sobre el tema "Human metagenomic"
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Rampelli, Simone <1985>. "Metagenomic trajectory of gut microbiome in the human lifespan". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6333/1/Rampelli_thesis_2014.pdf.
Texto completoRampelli, Simone <1985>. "Metagenomic trajectory of gut microbiome in the human lifespan". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amsdottorato.unibo.it/6333/.
Texto completoHuang, Kun. "Evolutionary analysis of the human microbiome using ancient metagenomic samples". Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/318833.
Texto completoGaudin, Maxime. "Human RNA bait library depletion for human (viral) pathogen discovery using shotgun metagenomic sequencing". Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0697/document.
Texto completoViral metagenomics, which is based on the random shotgun sequencing of all viral genomes present in a sample, is a promising approach for blind detection and identification of potential new pathogens. Its use is however still marginal because of the large proportion of human nucleic sequences. In this context, this thesis work aims at improving the metagenomic approach for the clinical diagnosis of viral infectious diseases by increasing the ratio of pathogen-to-host sequences trough depletion of human nucleic acids from the samples. The first chapter of this thesis consists in a bibliographic synthesis of viral metagenomic approaches in clinical research and the challenges we faced in this field. This bibliographic overview also includes a review article on targeted-enrichment sequencing approaches for pathogen detection in the field of human infectious diseases. The second chapter proposes a methodological development allowing the enrichment of non-human sequences from metagenomes through hybridization and capture of human nucleic acids with biotinylated human RNA probes. The third chapter is divided into two sub-chapters that propose the application of this protocol to the detection of putative pathogens in (1) a fatal case of encephalitis and (2) an enigmatic case of blood-culture negative infectious endocarditis. The methodological approach developed during this work is finally discussed in a fourth chapter, which also replaces the results obtained in the broader context of emerging infectious diseases and validation of the causal link between the agent detected and the observed pathology
Easton, S. "Functional and metagenomic analysis of the human tongue dorsum using phage display". Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/18512/.
Texto completoSzczepanska, Anna. "Functional metagenomic analysis of carbohydrate degrading enzymes from the human gut microbiota". Thesis, University of East Anglia, 2011. https://ueaeprints.uea.ac.uk/47983/.
Texto completoAl-Jarbou, Ahmed. "Metagenomic analysis of the human mouth virus population and characterisation of two lytic viruses". Thesis, University of Leicester, 2009. http://hdl.handle.net/2381/8221.
Texto completoTansirichaiya, Supathep. "Investigation of mobile genetic elements and antimicrobial resistance genes in human oral metagenomic DNA". Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/10041034/.
Texto completoTemisak, Sasithon. "Assessing the accuracy of metagenomic analysis of microorganisms involved in human diseases using control materials". Thesis, St George's, University of London, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.703283.
Texto completoAhiska, Bartu. "Reference-free identification of genetic variation in metagenomic sequence data using a probabilistic model". Thesis, University of Oxford, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.561121.
Texto completoZhu, Ana Cheng [Verfasser], Thomas [Gutachter] Dandekar y Peer [Gutachter] Bork. "Metagenomic analysis of genetic variation in human gut microbial species / Ana Cheng Zhu. Gutachter: Thomas Dandekar ; Peer Bork". Würzburg : Universität Würzburg, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-113890.
Texto completoZhu, Ana Cheng Verfasser], Thomas [Gutachter] [Dandekar y Peer [Gutachter] Bork. "Metagenomic analysis of genetic variation in human gut microbial species / Ana Cheng Zhu. Gutachter: Thomas Dandekar ; Peer Bork". Würzburg : Universität Würzburg, 2015. http://d-nb.info/1109750439/34.
Texto completoFancello, Laura. "A viral metagenomic approach to study taxonomic and functional diversity of viral communities from the environment to humans". Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5046/document.
Texto completoViruses are the most abundant and diverse organisms but little is known about their diversity. Recently, viral metagenomics has allowed performing broad unselective exploration of uncultivated viral communities, bypassing the limits of classical viral detection tools. However, most viral metagenomes are generated from temperate regions (for environmental studies) or from modern stool samples, sera/blood and naso-/oro- pharyngeal samples (for human-associated studies). Therefore, the purpose of my thesis is to study viral communities in the least investigated environments or human samples, using viral metagenomics.The first part of my thesis is a review of the main computational tools for the analysis of viral metagenomes. The second part of my thesis presents the first viromes generated from the Sahara desert. In the third part, I investigate human-associated viral communities: i) the first virome from a human coprolite; ii) the first viromes generated from human pericardial fluids, in idiopathic pericarditis cases; ii) a functional-level investigation of previously described viral metagenomes from cystic fibrosis patient sputa that focuses on antimicrobial resistance genes carried by bacteriophages to better understand the emergence of multidrug-resistance bacteria in the airways of cystic fibrosis patients.This thesis work provides original data on unexplored viral communities and shows the potential of viral metagenomics to give insights on viral diversity, reveal the presence of expected and unexpected viruses and decipher their role in the ecosystem
Plaza, onate Florian. "Reconstitution de pan-génomes microbiens par séquençage métagénomique aléatoire : Application à l’étude du microbiote intestinal humain". Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLV068/document.
Texto completoThe advent of shotgun metagenomic sequencing has revolutionized microbiology by allowing culture-independent characterization of complex microbial communities such as the human gut microbiota. Recently developed bioinformatics tools achieved strain-level resolution by making a census of accessory genes or by capturing nucleotide variants (SNPs). Yet, these tools are hampered by the extent of available reference genomes which are far from covering all the microbial variability. Indeed, many species are still not sequenced or are represented by only few genomes.Building of non-redundant gene catalogs followed by the binning of co-abundant genes reveals a part of the microbial dark matter by reconstituting the gene repertoire of species potentially unknown. While existing methods accurately identify core genes present in all the strains of a species, they miss many accessory genes or split them into small gene groups that remain unassociated to core genomes. However, capturing these accessory genes is essential in clinical research and epidemiology because they provide functions specific to certain strains such as pathogenicity or antibiotic resistance.In this thesis, we developed MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also.With MSPminer, we structured a catalog made up of 9.9 million genes of the human gut microbiota in 1 661 MSPs. The homogeneity of the taxonomic annotation, of the nucleotide composition as well as the presence of essential genes indicate that the MSPs do not correspond to chimeras but to biologically consistent objects grouping genes from the same species. Among these MSPs, 1 301 (78%) could not be annotated at species level showing that many microorganisms colonizing the human intestinal tract are still unknown despite the substantial improvements of microbial culture techniques. Remarkably, MSPs capture more genes than clusters generated by existing tools while ensuring high specificity.This set of MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In this way, we take advantage of the MSPs to compare the impact of two main types of surgeries, the laparoscopic sleeve gastrectomy (LSG) and the Roux-En-Y gastric bypass (LRYGB). Finally, the MSPs open the way to strain-level analyses. In another cohort, we identified subspecies associated the host geographical origin by studying presence/absence patterns of the accessory genes grouped in the MSPs
Ullmann, Leila Sabrina [UNESP]. "Pesquisa de genomas virais em primatas não humanos do novo mundo por metagenômica". Universidade Estadual Paulista (UNESP), 2014. http://hdl.handle.net/11449/123325.
Texto completoZoonoses emergentes com origem em animais selvagens representam a mais significante e crescente ameaça à saúde global. Os primatas não humanos contribuem com 20% das principais doenças humanas, são considerados o principal modelo experimental e também servem como sentinelas para diferentes doenças que acometem o homem. Os objetivos da presente tese foram desenvolver protocolos de metagenômica viral para detectar sequências de vírus a partir de plasma de primatas não humanos do Novo Mundo (Saimiri sciuratus, Aotus ainfulatus, Alouatta guariba e Sapajus apella) mantidos em cativeiro no Centro Nacional de Primatas (Belém, PA), no Refúgio Biológico Bela Vista (Foz do Iguaçu, PR) e no Parque Ecológico do Tietê (São Paulo, SP). A tecnologia Illumina (MiSeq) foi usada para o sequenciamento massivo e um fluxograma bioinformático foi desenvolvido para analisar as sequências obtidas. De forma geral, genomas correspondentes a diferentes famílias virais foram identificadas e ênfase foi dada ao torque teno vírus, ao vírus da hepatite G (tipos A e B), parvovírus e papilomavírus. Uma nova sequência de genoma completo do gênero Hepacivirus, família Flaviviridae, foi identificado em primatas do sul do Brasil. Os resultados demonstram a possibilidade de variedade de genomas virais presentes em primatas do Novo Mundo, considerados clinicamente saudáveis e destaca a importância de estudos que objetivam identificar possíveis vírus emergentes. Palavras-chave: doenças infecciosas emergentes, primatas não humanos do Novo Mundo, metagenômica viral, sequenciamento massivo e um fluxograma bioinformático foi desenvolvido para analisar as sequências obtidas. De forma geral,genomas correspondentes a diferentes famílias virais foram identificadas e ênfase foi dada ao torque teno vírus, ao vírus da hepatite G (tipos A e B), parvovírus e papilomavírus. Uma nova sequência de genoma completo do gênero Hepacivirus, família ...
Wild animals-borne emerging zoonoses represent the most significant and growing threat to global health. Non-human primates contribute with 20% of major human diseases, as they are considered the main experimental model and also can be considered sentinels for different diseases that affect humans. The aims of the present thesis were to develop a viral metagenomics protocol to detect sequences from viruses in plasma from captive New World non-human primate species (Saimiri sciuratus, Aotus ainfulatus, Alouatta guariba e Sapajus apella) from National Primate Center (Belém, PA), Bela Vista Biological Sanctuary (BVBS, Foz do Iguaçu, PR), and Tietê Ecological Park (São Paulo, SP). The Illumina technology (MiSeq) was used for deep sequencing, and a bioinformatics pipeline was developed in order to analyze the sequences obtained. Overall, genomes corresponding to different viral families were identified from plasma, and emphasis was given to torque tenus virus, hepatitis G virus types A and B, parvovirus, and pappilomavirus. A new whole-genome sequence from Hepacivirus genus, Flaviviridae family, was identified in monkeys from Southern Brazil. The results demonstrate the wide variety of viral genomes present on clinically healthy New World monkeys and highlight the importance of studies that aim to identify possible emerging viruses
Raguideau, Sébastien. "Analyse de données de métagénomique fonctionnelle par NMF pour la modélisation de la dégradation des fibres par le microbiote intestinal humain". Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLA027/document.
Texto completoThe purpose of this work of thesis is to model the capacity of degradation of non-digestible polysaccharides by the human intestinal microbiote. To this end we exploit metagenomic data. We use abundances of nucleotide sequences in 1408 samples whose metabolic function are assigned by annotation against a database. The sequences are annotated with functional markers. Upon manual selection of 86 functional markers relevant to the activity of metabolisation of polysaccharides, we their abundances variation among the metagenomic samples are studied.We propose an ecological approach in modeling the human intestinal microbiote. We consider the intense functional selection of this ecosystem and assume that identical cluster of metabolic functions can be found in different proportions in every human gut microbiota. We propose the term of functional assembly as to account for spacial and temporal co-occurence of functional cluster. In practice, theses assemblies are determined by their composition and can be interpreted as combinations of functional traits aggregated at the levels of the cluster of microorganisms composing each assembly. Functional assemblies are inferred by the means of Non-Negative Matrix Factorization (NMF). This method allows to determine the composition of functional assemblies and their abundance in each of the 1408 metagenomic sample.Furthermore, we exploit metabolic information from bibliographic resources and 190 microbial genomes in order to specify the composition of these functional assemblies. This information is translated in the form of a constraint.We find 4 assemblies by considering a consensus between various criteria. The use of metabolic information allow to interpret theses assemblies biologically. By exploiting the metadata of the 1408 samples, we observe a different behaviour for the samples coming from individuals suffering from Crohn disease. We validate this observation on external data.We proposed a reductionistic approach allowing to represent an important metabolic process at the level of the microbiota. We find a small number of 4 functional assemblies which are biologically likely and approach well the 1408 metagenomic samples
Zolfo, Moreno. "Metagenomics-based discovery of unknown bacteriophages In the human microbiome". Doctoral thesis, Università degli studi di Trento, 2020. http://hdl.handle.net/11572/275378.
Texto completoWard, Tonya L. "Characterizing Immune-modulatory Components of Human Milk: The Fate and Function of Soluble CD14 and the Human Milk Metagenome". Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31096.
Texto completoReynolds, L. J. "The identification and characterisation of novel antimicrobial resistance genes from human and animal metagenomes". Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1563757/.
Texto completoZimmerman, Brian D. "Human Mitochondrial DNA and Endogenous Bacterial Surrogates for Risk Assessment of Graywater Reuse". University of Cincinnati / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1397233273.
Texto completoThomas, Andrew Maltez. "Microbial community profiling of human gastrointestinal cancers". Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-07022019-134344/.
Texto completoO microbioma humano - definido como as comunidades microbianas que vivem sobre e dentro do corpo humano - está se tornando um fator cada vez mais importante em doenças humanas. O campo de estudo que investiga o papel do microbioma no desenvolvimento do câncer humano, denominado oncobioma, está crescendo e já levou a importantes descobertas como o papel da espécie Fusobacterium nucleatum na carcinogênese e progressão tumoral de tumores colorretais. Motivado por estas descobertas, esta tese de doutorado analisou o oncobioma por diferentes perspectivas, investigando se alterações nos perfis microbianos estavam associados à presença da doença ou a uma resposta adversa ao tratamento. Usamos tanto amostras de tecidos de biópsias e o sequenciamento do gene 16S rRNA (N = 36), quanto metagenomas fecais públicos e privados (N = 764), para investigar associações entre o microbioma e o câncer colorretal (CCR). Observamos um aumento significativo da riqueza microbiana no CCR, independentemente do tipo da amostra ou metodologia, que era em parte, devido ao aumento de espécies tipicamente presentes na cavidade oral. Observamos também um aumento da abundância de táxons específicos no CCR, que incluíam Bacteroides fragilis, Fusobacterium, Desulfovibrio e Bilophila. Analisando o potencial funcional dos metagenomas, encontramos um aumento significativo da enzima liase colina trimetilamina (cutC) no CCR, cuja associação era dependente de 4 variantes de sequência, demonstrando ser um possível novo mecanismo de carcinogênese no CCR. Assinaturas preditivas do microbioma treinadas na combinação dos estudos demonstraram ser altamente preditivas e consistentes nos diferentes estudos (média de AUC 0.83, mínimo de 0.81). Para investigar o possível papel do microbioma na resposta ao tratamento, analisamos os perfis microbianos do suco gástrico de pacientes com câncer gástrico (N = 36) antes e depois do tratamento quimioterápico neoadjuvante. As comunidades microbianas apresentaram uma variabilidade inter-individual notavelmente grande, com diminuições significativas na riqueza e diversidade filogenética pós tratamento, além de estarem associadas principalmente ao pH, mas também à resposta patológica e ao tempo da coleta. Os gêneros mais abundantes encontrados nos pacientes antes ou depois da quimioterapia incluíam Streptococcus, Prevotella, Rothia e Veillonella. Apesar das limitações inerentes às escolhas experimentais, esta tese proporciona assinaturas do microbioma que podem servir de base para testes clínicos prognósticos e estudos mecanísticos, além de dar mais suporte ao papel do microbioma oral em doenças humanas.
Rahman, M. A. "Detection and characterisation of integrons, gene cassettes and cassette-located antibiotic resistance genes in the human oral metagenome". Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1575642/.
Texto completoVeras, Henrique César Teixeira. "Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano". Universidade Católica de Brasília, 2013. https://bdtd.ucb.br:8443/jspui/handle/tede/2473.
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Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually.
Humanos vivem em constante associação com microrganismos. A quantidade de microrganismos presentes no corpo humano ultrapassa o nosso próprio número de células. Essa comunidade de microrganismos tem profunda influência na saúde e doenças. As tecnologias de sequenciamento de DNA de alta capacidade e abordagens moleculares independente de cultura têm ampliado a compreensão acerca das comunidades de microrganismos e a associação destes com o hospedeiro. O trato gastrointestinal humano abriga uma das mais complexas comunidades bacterianas. Foi proposto recentemente que o microbioma pode ser categorizado em três enterotipos. No nosso estudo, utilizamos dados metagenômicos quantitativos buncando identificar padrões filogenéticos no microbioma intestinal para desenvolver modelos de predição para os enterotipos. Para alcançar este objetivo, testes estatísticos foram aplicados aos dados referente a abundância de bactérias em nível taxonômico correspondente a gênero. Identificamos gêneros com a abundância significativamente diferente e correlações importantes. Além da razão entre gêneros para ser utilizada como parâmetro bioindicativo dos respectivos enterotipos. Através do teste de regressão logística identificamos que o modelo de predição para o ET1 foi influenciado significativamente pela razão de Bacteroides / (Prevotella + Ruminococcus). No modelo para predição do ET2, foi a razão de Prevotella / Bacteroides que apresentou significância. E para o modelo do ET3, identificamos a razão de (Akkermansia + Alistipes) / (Bacteroides + Prevotella) como parâmetro significativo. Estes modelos foram avaliados contra dois conjuntos de dados independentes e associados com o valor de cut-off 5%; 20% e; 95% respectivamente. Além do valor de cut-off para cada modelos, a validação cruzada permitiu a associação do modelo com as medidas de PPV para o ET1, especificidade para o ET2 e PNV para o ET3. Propomos a validação experimental destes modelos pela técnica de qPCR. E com essa metodologia estabelecida, seria possível fazer o diagnóstico do enterotipo individualmente.
Ullmann, Leila Sabrina. "Pesquisa de genomas virais em primatas não humanos do novo mundo por metagenômica /". Botucatu, 2014. http://hdl.handle.net/11449/123325.
Texto completoCoorientador: Alexander Welker Biondo
Banca: Maria Inês de Moura Campopos Pardini
Banca: Deilson Elgui de Oliveira
Banca: Jean Carlos Ramos da Silva
Banca: Walfrido Kuhl Svoboda
Resumo: Zoonoses emergentes com origem em animais selvagens representam a mais significante e crescente ameaça à saúde global. Os primatas não humanos contribuem com 20% das principais doenças humanas, são considerados o principal modelo experimental e também servem como sentinelas para diferentes doenças que acometem o homem. Os objetivos da presente tese foram desenvolver protocolos de metagenômica viral para detectar sequências de vírus a partir de plasma de primatas não humanos do Novo Mundo (Saimiri sciuratus, Aotus ainfulatus, Alouatta guariba e Sapajus apella) mantidos em cativeiro no Centro Nacional de Primatas (Belém, PA), no Refúgio Biológico Bela Vista (Foz do Iguaçu, PR) e no Parque Ecológico do Tietê (São Paulo, SP). A tecnologia Illumina (MiSeq) foi usada para o sequenciamento massivo e um fluxograma bioinformático foi desenvolvido para analisar as sequências obtidas. De forma geral, genomas correspondentes a diferentes famílias virais foram identificadas e ênfase foi dada ao torque teno vírus, ao vírus da hepatite G (tipos A e B), parvovírus e papilomavírus. Uma nova sequência de genoma completo do gênero Hepacivirus, família Flaviviridae, foi identificado em primatas do sul do Brasil. Os resultados demonstram a possibilidade de variedade de genomas virais presentes em primatas do Novo Mundo, considerados clinicamente saudáveis e destaca a importância de estudos que objetivam identificar possíveis vírus emergentes. Palavras-chave: doenças infecciosas emergentes, primatas não humanos do Novo Mundo, metagenômica viral, sequenciamento massivo e um fluxograma bioinformático foi desenvolvido para analisar as sequências obtidas. De forma geral,genomas correspondentes a diferentes famílias virais foram identificadas e ênfase foi dada ao torque teno vírus, ao vírus da hepatite G (tipos A e B), parvovírus e papilomavírus. Uma nova sequência de genoma completo do gênero Hepacivirus, família ...
Abstract: Wild animals-borne emerging zoonoses represent the most significant and growing threat to global health. Non-human primates contribute with 20% of major human diseases, as they are considered the main experimental model and also can be considered sentinels for different diseases that affect humans. The aims of the present thesis were to develop a viral metagenomics protocol to detect sequences from viruses in plasma from captive New World non-human primate species (Saimiri sciuratus, Aotus ainfulatus, Alouatta guariba e Sapajus apella) from National Primate Center (Belém, PA), Bela Vista Biological Sanctuary (BVBS, Foz do Iguaçu, PR), and Tietê Ecological Park (São Paulo, SP). The Illumina technology (MiSeq) was used for deep sequencing, and a bioinformatics pipeline was developed in order to analyze the sequences obtained. Overall, genomes corresponding to different viral families were identified from plasma, and emphasis was given to torque tenus virus, hepatitis G virus types A and B, parvovirus, and pappilomavirus. A new whole-genome sequence from Hepacivirus genus, Flaviviridae family, was identified in monkeys from Southern Brazil. The results demonstrate the wide variety of viral genomes present on clinically healthy New World monkeys and highlight the importance of studies that aim to identify possible emerging viruses
Doutor
Alves, Renato [Verfasser] y Peer [Akademischer Betreuer] Bork. "Integrating metatranscriptomes and metagenomes for deconvolution of composition and expression in human gut and artificial communities / Renato Alves ; Betreuer: Peer Bork". Heidelberg : Universitätsbibliothek Heidelberg, 2020. http://d-nb.info/1223098532/34.
Texto completoPatrascu, Isabelle. "Description des systèmes enzymatiques du microbiote iléal humain associés à la dégradation des fibres alimentaires et exploration du microbiote fécal d'un individu obèse : approche de métagénomique fonctionnelle et recherche de glycoside hydrolases inédites". Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS098.
Texto completoAmong the crucial functions of the intestinal microbiota, extracting energy from food such as dietary fibres is of major importance. Facing the huge diversity of incoming complex carbohydrates, the fibrolytic bacteria synthesize a set of diversified Carbohydrate-Active Enzymes (CAZymes) including Glycoside Hydrolases (GH) that specifically disrupt complex polysaccharides. Here, using functional metagenomic approaches, we explored the organization and properties of bacterial enzymatic systems involved in the breakdown of plant cell wall (PCW) glycans in the intestinal tract.Firstly, we investigated the capacity of the microbiota associated to the human ileum mucosa to degrade complex non-starch polysaccharides in a healthy context. This function has never been investigated in this part of the intestine, but it has been rather associated to microorganisms inhabiting the colon, due to more accessible fecal samples. Using a fosmid library derived from a healthy part of the human ileal mucosa, we screened 20,000 metagenomic clones for their activities against carboxymethylcellulose and xylan chosen as models of the major PCW polysaccharides from dietary fibres. Twelve positive clones revealed a broad range of CAZyme encoding genes from Bacteroides to Clostridiales species, as well as Polysaccharide Utilization Loci (PUL). Functional GH genes were identified and break-down products examined from different polysaccharides including mixed-linkage β-glucans. Revealed CAZymes and PUL were also examined for their prevalence in human gut microbiomes. Part of them belongs to unidentified strains rather specifically established in the ileum. Others were enzymes unclassified in identified GH families or with original properties addressing novel candidates for biotechnological applications. Thus, we evidenced for the first time that the ileal mucosa associated-microbiota encompasses the enzymatic potential for PCW complex polysaccharide degradation that might start in the small intestine.In a second time, by using the same methodology, we harvested the enzymatic capacities of the fecal microbiota from an obese person to disrupt complex polysaccharides from dietary fibres usually consumed in lower quantity in obese people. This study aimed at examining the links between genes encoding enzymes specifically dedicated to PCW complex carbohydrates and the obese phenotypic status using reference microbial gene catalogs. We screened a fecal metagenomic library from an obese individual on representative PCW substrates and identified 50 clones belonging to 14 different species from the Bacteroidetes, Firmicutes and Actinobacteria phyla. The metagenomic inserts harbor genes encoding enzymes from GH families specific from complex carbohydrate degradation. First querying of the prevalence of these genes in hundreds individuals (obese and control), using catalogs of reference microbial genes, suggest associations with the "obese" phenotypic status
Dobrijevic, Dragana. "Functional analysis of the predicted surface proteome of Gram-positive bacteria from the human gastrointestinal tract. A high-throughput approach to identification of immune modulators". Thesis, Paris 11, 2013. http://www.theses.fr/2013PA112182.
Texto completoIt is now well established that the human gastrointestinal tract microbiota plays an intricate role in human health. However, we are only beginning to understand the molecular mechanisms by which bacteria act on the host cells, knowledge that could provide new directions in treating and preventing disease. The last decade has seen a rapid development of the gut microbiota field, and presently abundant metagenome data and hundreds of genome sequences of individual commensal bacteria are available. Together, these data provide a platform for in silico mining approaches to identify bacterial molecules involved in communication with the host. The challenge is to develop efficient mining and validation strategies, in order to move from correlations and predictions to experimentally validated functional bacteria – host relationships. The work presented in this thesis aims to demonstrate the importance of in silico analyses to broaden our knowledge on bacteria - host interactions. It also shows how this information can be applied in functional studies aiming to identify functional bacterial effector molecules. The main results can be divided in three parts. The first part deals with the development and validation of a host - vector system for functional (meta)genomics studies. The second part describes a functional study where a number of candidate effectors were identified among secreted and surface-exposed proteins from Gram-positive bacteria using an in silico mining approach. It also describes the application of the newly developed host - vector system to evaluate the role of these candidates in immune modulation. Finally, in the third part we present an in silico study that identified new bacterial functions over- or under-represented in a selection of Gram-positive human gut bacteria
Andrew, Brandon E. "DETERMINATION OF STRATEGIC PRIORITIES FOR A MICROBIOME COMPANY THROUGH ANALYSIS OF TECHNICAL CAPABILITIES AND CURRENT MARKET LANDSCAPES". Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1586527376213742.
Texto completoFadlallah, Jehane. "Impact du déficit en IgA sur la symbiose hôte/microbiote intestinal chez l'homme". Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066740/document.
Texto completoIgA responses play a key role in gut mucosa, defending host against pathogens but also shaping the commensal flora. In order to get insights into the specific contributions of IgA to host/microbial symbiosis in humans, we explored patients that lack only IgA, using gut microbial metagenomics and systems immunology. Microbiota composition was compared between 34 healthy controls and 17 selective IgA deficiency (sIgAd) patients. Contrary to what was observed in murine models of IgA deficiency, we show that human sIgAd is not associated with massive perturbations of gut microbial ecology, regarding phyla distribution, bacterial diversity and gene richness. A clear gut microbial signature is however associated to sIgAd: we found 19 over-represented MGS mainly described to be pro-inflammatory, but also 14 under-represented MGS, mainly known to be beneficial. We also explored local consequences of IgA deficiency, particularly whether IgM could replace IgA at host/bacterial interface. Using a combination of bacterial flow sorting and DNA sequencing, we therefore analysed the composition of IgM-coated microbiomes observed in sIgAd. We show that IgM only partially supply IgA deficiency, as not all typical IgA targets can also be opsonized by IgM, but nevertheless contribute to maintain Actinobacteria diversity. IgA deficiency is associated with a skewed circulating CD4+ T cell profile towards TH17, as well as markers of bacterial translocation. Finally, sIgAd is associated with a perturbation of the minimal bacterial network. Altogether our results suggest that human IgA deficiency is associated with a mild dysbiosis associated to systemic inflammation despite the presence of IgM
Almeida, Mathieu. "Caractérisation de flores microbiennes intestinale humaine et fromagère par méthode de métagénomique quantative". Thesis, Paris 11, 2013. http://www.theses.fr/2013PA112076/document.
Texto completoThe microbial flora is a micro-organism complex containing for example bacteria, archaea, lower eukaryotes and viruses, which play an important role in ecosystem equilibrium. This flora remains poorly defined as in 2012, only ~30% of the intestinal flora micro-organisms have been characterized, and less than 50% of traditional cheese floras were characterized at the functional level. Since 2006, the second generation of DNA sequencers have allowed the direct analysis of the genetic content from a microbial flora sample without isolation or culture limitation. However, the DNA reads generated are not structured with respect to genomes and also are highly fragmented, slowing down dramatically the exploitation and analysis of these data.In this work, a new methodology based on quantitative metagenomic are described., This allows the clustering of short DNA sequences with the same abundance in multiple metagenomic samples, which should originate from the same microbial species. A 3.9 million gene catalog has been built from the human intestinal tract microbiota and divided into 741 units or clusters corresponding to bacteria, archaea and eukaryote genomes. These have been defined as metagenomic species (MGS) and 6640 units of them corresponds mainly to viral genomes, plasmids and genetic islands like CRISPR, with the sub-name of metagenomic units (MGU). This methodology was then used to facilitate the association analysis of the intestinal flora composition with human diseases such as Crohn’s disease, obesity or type 2 diabetes. Within, the alimentary flora, our methods have also been used to constitute a 134 genomic catalog of cheese bacteria and characterize them from the surface of traditional cheeses. This allowed the detection of new alimentary bacteria, that will enriched the list of bacteria with potential interest for the commercial exploitation of fermented products
Bellali, Sara. "Évaluation de l'impact de la conservation sur la viabilité et la cultivabilité du microbiote intestinal humain". Thesis, Aix-Marseille, 2019. http://theses.univ-amu.fr.lama.univ-amu.fr/191121_BELLALI_58q14hn462lvr402balo_TH.pdf.
Texto completoThe human gut microbiota harbors a wide range of microorganisms that play a crucial role in human health. However, the number of bacterial cells detected by quantitative culture-independent methods was found to be much higher compared to that of cultured bacteria on agar plates. That discrepancy is known as the “ Great plate count anomaly ”. The main goal of this work was to investigate the “ unculturability ” of gut bacteria and maintain their viability. we found that exposure to oxygen for more than 1 hour decreased the culturability of bacteria to 50%. More importantly, when samples were exposed to oxygen for less than 2 min, the culturability increased to 87%. This result suggested that the non-culturability might be due to the fact that oxygen-sensitive cells were in the viable but non-culturable state, or either injured or dead. This funding was confirmed when we sequenced the FACS sorted live, injured and dead bacteria, where, 28% of of bacterial OTUs in total fecal samples were exclusively found dead and/or injured. Among these non-live bacteria, about two-thirds were unknown, thus a large amount were anaerobic. In the other hand, our new protectant medium showed its effectiveness on fecal samples and oxygen sensitive bacteria. In conclusion, our work has confirmed the importance of sample conditioning and processing to obtain the best culture conditions and isolation rates. In addition, our study allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approach are needed for full insight into the diversity and richness of culturable and unculturable bacteria in the human gut microbiota
Mkaouar, Héla. "Rôle des serpines, inhibiteurs de protéases à serine, du microbiote digestif humain dans les maladies inflammatoires de l'intestin". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS108.
Texto completoSerine protease inhibitors (Serpins) are a class of proteins that reamin poorly studied in bacteria. In this thesis we are interested in the study of serpins originating from the intestinal microbiota and the investigation of their anti-inflammatory potential for the treatment of inflammatory bowel diseases (IBD) in humans. For this we have identified serpins from the human gut microbiota and analyzed their diversity as well as their distribution between healthy and IBD patients. These data allowed isolating serpins significantly associated with IBD. The purification of four of them led us to demonstrate that they inhibit human proteases involved in IBD. Biochemical and kinetic analysis of these proteins showed that they exhibit original properties, in particular their high inhibition efficiency. The study of the protective effect of three serpins in an animal model of colitis demonstrated for the first time the efficacy of serpins in vivo demonstrating thus their therapeutic potential
Arumugam, Manimozhiyan. "Comparative metagenomic analysis of the human intestinal microbiota". Doctoral thesis, 2010. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-55903.
Texto completoDer menschliche Darm beheimatet tausende Mikroben, die für das menschliche Leben wichtig sind. Da die meisten dieser Mikroben nicht kultivierbar sind, ist „Metagenomics“ ein wichtiges Werkzeug zum Verständnis dieser wichtigen mikrobiellen Gemeinschaft. Um vergleichende Metagenomanalysen durchführen zu können, habe ich das Computerprogramm SMASH (Simple metagenomic analysis shell) entwickelt. SMASH kann auch zur Assemblierung und Analyse von Einzelgenomen benutzt werden und wurde erfolgreich auch das Bakterium Mycoplasma pneumoniae und den Pilz Chaetomium thermophilum angewandt. Im Zusammenhang mit der Beteiligung unserer Arbeitsgruppe am MetaHIT (Metagenomics of the human intestinal tract) Konsortium, habe ich SMASH benutzt um die Assemblierung zu validieren und die Fehlerrate der Assemblierung von 576.7 Gb Metagenomsequenzen, die mit der Illumina Solexa Technologie aus der fäkalen DNS von 124 europäischen Personen gewonnen wurde, zu bestimmen. Des Weiteren habe ich die Vollständigkeit des Genkatalogs dieser Metagenome, der 3.3 Millionen offene Leserahmen enthält, geschätzt. Zuletzt habe ich SMASH benutzt um die Darmmetagenome von 39 Personen aus 6 Ländern zu analysieren. Hauptergebnis dieser Analyse war, dass die Variation der Darmmikrobiota nicht kontinuierlich ist. Anstatt dessen fanden wir so genannte Enterotypen. Enterotypen sind komplexe Zustände der Symbiose zwischen Wirt und Mikroben, die sich nicht durch Wirteigenschaften, wie Alter, Body-Mass-Index, Erkrankungen und Ernährungseigenschaften oder ein mögliches technisches Bias erklären lassen. Das Konzept der Enterotypen könnte weitgehende Folgen haben. Diese könnten zum Beispiel die unterschiedlichen Reaktionen auf Diäten oder Medikamenteneinahmen erklären. Weiterhin konnten wir eine Anzahl an Markern im menschlichen Darmmikrobiome finden, die mit unterschiedlichen Wirtseigenschaften wie dem Body-Mass-Index korrelieren. Dies hebt die Wichtigkeit dieser Analysemethode hervor und erweckt Hoffnungen auf Anwendung mikrobieller Marker als diagnostisches oder sogar prognostisches Werkzeug für menschliche Erkrankungen in denen das Mikrobiom eine Rolle spielt
BACCI, GIOVANNI. "Mining Microbiomes. Computational Biology approaches to uncover the complexity of bacterial communities". Doctoral thesis, 2015. http://hdl.handle.net/2158/986409.
Texto completoZhu, Ana Cheng. "Metagenomic analysis of genetic variation in human gut microbial species". Doctoral thesis, 2015. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-113890.
Texto completoMikrobielle Arten (Bakterien und Archaeen) im menschlichen Darm sind wichtige Begleiter für unsere Gesundheit. Jedoch gibt es nicht nur starke Unterschiede zwischen individuellen Wirten in der Artenzusammensetzung des Darmmikrobioms, sondern es scheint sogar Individuen-spezifische Bakterienstämme zu geben. Analysen von Bakterien wie z.B. Escherichia coli haben schon früh gezeigt, dass die Genome von Bakterienstämmen derselben Art große Unterschiede aufzeigen können; jedoch wurden diese Unterschiede bisher noch nicht in einer natürlichen Umgebung gezeigt. Genetische Variation kann viele Ausprägungen haben und reicht von kleinen Veränderungen wie „small nucleotide polymorphism“ (SNP) zu makroskopischen Veränderung, wie z.B. chromosomalen Restrukturierungen. All diese genetischen Variationen wurden bis jetzt nicht in der natürlichen Umgebung der Bakterien studiert, vorallem bedingt durch fehlende Methoden um die meisten dieser Bakterien um Labor zu kultivieren. Metagenomische Studien können hier helfen, da sie unabhängig von Kultivierungen jegliche DNS aus einer natürlichen Bakteriengemeinschaft untersuchen. Jedoch wurde dies in den meisten bisher veröffentlichten metagenomischen Studien nicht ausgenutzt da diese hauptsächlich auf die Anzahl der gefunden Gene ausgerichtet waren. Das Ziel meiner Doktorarbeit war es, die genetische Variation in Darmbakterien zu beschreiben und phenotypische Veränderungen zu untersuchen. Dies habe ich umgesetzt durch die Erforschung (1) der SNP-Varianz in Darmbakterien, mit besonderem Augenmerk auf Gene, die unter einem selektivem Druck stehen und (2) der Variationen in der Genzusammensetzung eines Genomes (als eine Annäherung an strukturelle Variationen) und welchen Effekt dies auf Mikrobenarten und Wirtsphenotypen hat. Im ersten Kapitel meiner Doktorarbeit beschreibe ich meine Arbeit in einem Projekt unserer Gruppe, in dem wir basierend auf metagenomischen Daten 10 Millionen SNPs in menschlichen Darmbakterien beschrieben haben. Diesen Datensatz habe ich verwendet um die erste SNP-basierte, vergleichende Studie der Bakterienevolution in einem natürlichen Habitat zu realisieren. Ich entdeckte, dass Bakterienstämme unabhängig vom Wirt ähnliche evolutionäre Raten haben. Genauer gesagt, die evolutionäre Rate für eine Art ist stabiler zwischen Wirten, als die von verschiedenen Spezies innerhalb eines Wirtes. Ausserdem fand ich heraus, dass die Evolution von einzelnen Genen unabhängig vom restlichen Genom einer Spezies ist. Dies könnte durch einen Selektionsdruck wie z.B. die Ernährung des Wirtes ausgelöst werden, was ich am Beispiel des Galactokinasegenes (galK) gezeigt habe. Obwohl wir zeigen konnten, dass das SNP-Profil der Darmbakterien spezifisch für den jeweiligen Wirt ist, konnten wir keine Assoziation zwischen SNPs und Wirtsphänotypen finden. Auch aus diesem Grund habe ich mich in meiner weiteren Arbeit verstärkt auf makroskopische Genomvariationen konzentriert. Im zweiten Teil meiner Doktoarbeit entwickelte ich eine neue Methode, um Variationen in der genomische Zusammensetzung von einzelnen Bakterienarten zu beschreiben, wieder basierend auf metagenomischen Daten. Hierbei fokussiere ich mich insbesondere auf Gene, die in unseren metagenomischen Daten im Verglich zum Referengenom fehlen und wende dies auf die 11 dominantesten Bakterienspezies an. Diese neue Methode ist robust, da die gefundene Genomvarianz in unseren metagenomischen Daten übereinstimmt mit Daten aus komplett sequenzierten Genomen. So konnte ich herausfinden, dass im Durchschnitt 13% der Gene einer Bakterienart zwischen einzelen Wirten varieren. Besonders interessant ist hier, dass wir keine zwei Wirte gefunden haben, die für eine Bakterienart genau diesselben Gene haben. Jedoch ist die erwarte Varianz aller Wahrscheinlichkeit nach noch größer, da ich mit dieser Methode nur fehlende Gene beschreiben kann, aber nicht neu hinzugekommende. Diese Varianz kann auch wichtige bakterielle Funktionen betreffen, z.B. Gene für „polysaccharide utilization loci“ (PULs) und „capsular polysaccharide synthesis“ (CPS), welche wichtig sind um Ballaststoffe in der Nahrung zu verwerten. Zusammenfassend konnte ich in dieser Arbeit zeigen, dass metagenomische Methoden robust genug sind um die genetische Varianz von Darmbakterien zu beschreiben. Ausserdem konnte ich zeigen, dass die beschriebene Varianz benutzt werden kann, um phenotypische Veränderungen von Bakterien vorherzusagen (demonstriert für die galK, PULs and CPS-Gene). Dies wiederrum könnte benutzt werden um Vorhersagen für den Wirt über z.B. seine Ernährung zu machen. Meine Doktorarbeit zeigt wie wichtig es ist, einzelne Bakterienstämme zu charakterisieren, ganz analog zu der Bedeutsamkeit der genetischen Varianz des menschlichen Genomes
Escudeiro, Pedro Miguel Agostinho. "Metagenomic mining of pathogenicity and antibiotic resistance traits across human populations worlwide". Master's thesis, 2016. http://hdl.handle.net/10451/25543.
Texto completoO microbiota humano (a soma de todos os microrganismos que colonizam o corpo humano) ´e composto aproximadamente por 1e+14 células bacterianas, que abrangem vários taxa, e colonizam principalmente a pele, mucosas, tecido conjuntivo, e o tracto gastrointestinal, nomeadamente o cólon. O somatório de todos os genomas microbianos que lhe dizem respeito é frequentemente denominado microbioma. O conjunto de genes que codificam virulência (eventualmente conferindo patogenicidade à bactéria) são frequentemente codificados em elementos genéticos móveis. Deste modo, muitos factores de virulência (VF) bacteriana conseguem ser facilmente disseminados em populações bacterianas por transferência horizontal de genes (movimento de material genético entre células), convertendo batérias mutualistas ou comensais em potenciais patogenes. Analogamente, a coleção de genes cujos determinantes (produtos génicos) conferem resistência a antibióticos (AR), existentes tanto em bactérias patogénicas como não-patogénicas, também se apresenta repetidamente codificada em elementos genéticos móveis, os quais sob pressão selectiva, se conseguem disseminar por entre comunidades bacterianas através do processo de transferência horizontal de genes, atravessando por vezes as barreiras taxonómicas de espécie e género. Esta característica permite que a comunidade sobreviva, e persista como um todo, comportando-se como um reservatório de genes conferentes de resistência. Microbiomas ambientais, como os que se encontram presentes no solo, são descritos como reservatórios abundantes de genes de resistência a antibióticos. Estes codificam para determinantes de resistência a todas as classes de antibióticos descritas até hoje. Apesar da antibioticoterapia ser direcionada a bactérias patogénicas, esta também afeta muitas espécies bacterianas não-patogénicas que fazem parte do microbiota dos indivíduos sujeitos a este tipo de terapia medicamentosa. Efeito que também se verifica em bactérias ambientais que se encontrem expostas a este tipo de pressão selectiva consequente de más práticas agrárias e da pecuária, ou simplesmente poluição antropológica. Por conseguinte, o microbioma humano detém genes de resistência passiveis de transmissão a estirpes patogénicas, tornando-o num repertório de determinantes de resistência a antibióticos altamente diversificado. O estilo de vida virulento, característico de bactérias patogénicas, tem sido consecutivamente associado a fenótipos de resistência a antibióticos. No entanto, esta associação nem sempre tem sido direta e previsível. Por um lado, o crescente uso de antibióticos tem vindo a seleccionar bactérias detentoras de fenótipos resistentes, sejam elas patogénicas ou não, criando reservatórios genéticos de resistência em diversos microbiomas. Porventura não é claro se a diversidade de genes conferentes de virulência se correlaciona com a diversidade dos que conferem resistência a antibióticos. Em contrapartida, existem inúmeros relatos bibliográficos de estirpes altamente virulentas e multi-resistentes (resistentes a mais do que uma classe de antibiótico) que têm vindo a disseminar-se por todo o globo. Tendo em conta que atualmente existe uma grande disponibilidade de antibióticos, e em alguns casos, administração não supervisionada, podemos concluir que os microbiotas humanos, bem como os seus respectivos microbiomas, estão sujeitos a diferentes graus de pressões seletivas impostas pelos referidos compostos. Neste contexto, podemos inferir que para alguns patogenes, em ordem a sobreviver e colonizar o hospedeiro, codificar apenas para virulência pode não ser suficiente, se se encontrarem na presença de antibióticos. Por outras palavras, sob o efeito de pressões seletivas impostas pela administração de antibióticos, a seleção de elementos genéticos móveis que codifiquem para resistência aos referidos compostos juntamente com características genotípicas que confiram virulência irá ocorrer, tendo como consequência a sua disseminação dentro de comunidades bacterianas pertencentes ao microbiota humano. Tanto quanto sabemos, não existem registos bibliográficos sobre a dinâmica evolutiva que dita a epidemiologia de genes conferentes de resistência a antibióticos, e os que conferem virulência, colectivamente. Assim sendo, a presente dissertação pergunta se sob o efeito de pressões selectivas exercidas por antibióticos, os determinantes de resistência e de virulˆencia se encontram co-representados tanto em diversos microbiomas ambientais, como em microbiomas provenientes do trato gastrointestinal humano. Deste modo, foram escolhidos metagenomas a fim de abordar esta temática por várias razões. A mais preeminente prende-se com o facto das bactérias serem organismos sociais, vivendo em comunidades. Um metagenoma corresponde à panóplia de material genético isolado de uma comunidade, e posteriormente sequenciado, pelo que caracteriza o repertório completo de genes envolvidos em processos metabólicos, fisiológicos e ecológicos, como por exemplo, na adaptação ao ambiente pelas comunidades microbianas presentes na respectiva amostra sequenciada. Subsequentemente, a prospeção de genes em metagenomas surge como uma metodologia fidedigna no que toca ao estudo das pressões seletivas a que uma dada população bacteriana foi sujeita, assim como ao estudo da co-seleção de características genéticas do microbiota amostrado como um todo. No presente trabalho utilizamos 64 metagenomas ambientais, referentes a 12 biomas diversos, bem como 110 metagenomas do trato gastrointestinal humano, originários de indivíduos pertencentes a várias comunidades dos Estados Unidos da América, Venezuela, e Malawi, caracterizando várias faixas etárias, diferentes culturas, hábitos alimentares, bem como diferentes graus de acesso a saneamento básico, a cuidados médicos e antibióticos. Todos os metagenomas encontram-se publicamente disponíveis para download no servidor MG-RAST, tendo sido descarregados em ficheiros individuais em formato FASTA, nos dias 3 de Abril de 2015 (metagenomas do trato gastrointestinal humano) e 17 de Novembro de 2015 (metagenomas ambientais). Cada ficheiro compreende sequências proteicas previamente agrupadas a 90% de homologia pela pipeline de formatação de ficheiros do servidor MG-RAST, contendo assim sequências traduzidas não redundantes, e representando deste modo a diversidade proteica de cada metagenoma. O programa BLASTP foi utilizado a fim de inferir homologia de sequências proteicas envolvidas no fenómeno de resistência a antibióticos, bem como de virulência, de entre os metagenomas escolhidos, fazendo uso de duas bases-de-dados públicas: Resfams AR Proteins database (base-de-dados de proteínas bacterianas conferentes de resistência a antibióticos), e VFDB (base-de-dados de proteínas bacterianas envolvidas em virulência). Este programa permite inferir homologia entre sequências comparadas por via de um algoritmo de alinhamento de sequências derivado do algoritmo original de Smith-Waterman. De entre os vários critérios de seriação aplicáveis foi escolhido um limiar de E-value = 1e-15, com um filtro posterior que apenas considera o melhor alinhamento para cada sequência proteica, e que satisfaça os requisitos mínimos de 60% de homologia sob 75% de alinhamento entre sequências comparadas. Ulteriormente ainda se removeram os alinhamentos resultantes de sequências proteicas que tanto eram homologas de determinantes de resistência a antibióticos como de factores de virulência, de modo a eliminar um viés na análise estatística consecutivamente implementada. Seguidamente, de modo a aferir o tipo de relação entre os caracteres genéticos em causa, as contagens das diferentes sequências proteicas homologas de determinantes de resistência a antibióticos (ARd) foram correlacionadas numa primeira fase com o número de sequências proteicas presentes em cada metagenoma, previamente agrupadas a 90% (tamanho do metagenoma), procedendo de igual forma para as contagens de diversidade de sequências proteicas homologas de factores de virulência (VFd), para ambos os grupos de metagenomas considerados. Posteriormente as contagens ARd e VFd foram correlacionadas entre si, após a estandardização das mesmas. Em ordem a medir o grau de associação entre as correlações previamente descritas recorreu-se a medidas estatísticas como o coeficiente de correlação e o rho de Spearman, bem como o seu P-value. Foram também geradas todas as possíveis associações entre as contagens de ARd e VFd para subfamílias proteicas funcionais caracterizadas nas bases-de-dados mencionadas, efetuando uma correção aos P-values resultantes do rho de Spearman pelo procedimento de Benjamini-Hochberg. Em ordem a testar a dissemelhança entre médias provenientes dos rácios estandardizados de ARd/VFd em função da idade dos indivíduos pertencentes ao grupo de metagenomas do trato gastrointestinal humano, foram aplicados Welch Two Sample t-tests por pares, de acordo com os respectivos países de origem. Os nossos resultados mostram que os determinantes de resistência a antibióticos, bem como os factores de virulência, se encontram amplamente disseminados tanto em microbiomas ambientais, como em microbiomas do trato gastrointestinal humano pertencentes aos 110 indivíduos saudáveis originários de países diferentes. Em segundo lugar, também sugerem que, apesar das comunidades bacterianas ambientais possuírem maior variação de ARd e VFd tendo em conta o tamanho dos metagenomas, as comunidades que habitam o trato gastrointestinal humano detêm uma dependência linear muito forte no que toca à distribuição de ARd de acordo com o tamanho dos metagenomas, e uma relação linear forte entre VFd e o tamanho dos mesmos. Adicionalmente constatamos que as contagens estandardizadas de ARd e VFd apresentam uma correlação muito forte entre si nos metagenomas de origem ambiental, sendo que estas contagens também se mostraram fortemente correlacionadas no grupo de metagenomas provenientes do trato gastrointestinal humano. Entre os metagenomas do grupo anterior, os referentes aos indivíduos originários dos Estados Unidos da América, apresentam uma ampla diversidade de associações, ao passo que as amostras provenientes de indivíduos Venezuelanos não possuem uma associação estatisticamente relevante. No entanto, os metagenomas pertencentes a indivíduos Malauianos retratam a correlação e associação linear mais forte de entre os três países amostrados, possuindo também duas vezes mais contagens de ARd por VFd que os outros dois países. Referindo-nos ainda ao mesmo conjunto de metagenomas, conseguimos verificar que as contagens estandardizadas de ARd e VFd aparentam decrescer com o aumento da idade dos indivíduos, enquanto que os rácios ARd/VFd afiguram-se relativamente estáveis, evidenciando um incremento comum durante o primeiro ano de vida. Relativamente a todas as associações geradas entre subfamílias de proteínas que codificam para AR e as que codificam VFs, aquelas que se relacionam com o envelope celular bacteriano apresentaram as melhores correlações e estatísticas correspondentes. É de salientar que os resultados descritos neste trabalho apenas fornecem evidência para a co-representação de determinantes de AR e VF entre os metagenomas ambientais e do trato gastrointestinal humano que foram amostrados. Visto que a inclusão ou proximidade de determinantes AR e VF nos mesmos elementos genéticos m´oveis não se prende com os objectivos da presente dissertação, os nossos resultados não podem confirmar que a mobilização dos demais determinantes esteja a ocorrer conjuntamente. De qualquer modo, a natureza co-representativa dos nossos resultados reforça a noção, bem como a hipótese de co-seleção dos referidos determinantes.
Genes contributing to the pathogenicity of a particular bacterial species are often grouped in pathogenicity islands, and encoded on mobile genetic elements such as plasmids or phages, as happens with some genes coding for resistance to antibiotics. Pathogenic bacteria have gradually become resistant to antibiotics as a result of intense selective pressure they are subjected to. Here we provide evidence that further reinforces the hypothesis on which, under antibiotics selective pressure, resistance and virulence traits are co-selected amongst bacterial communities naturally occurring in the human gut microbiome. Through means of metagenome mining, we have studied 64 environmental metagenomes from 12 diverse biomes, as well as 110 human gut metagenomes issuing from individuals belonging to different human populations across the world, having contrastive cultural, dietary and sanitary lifestyles, along with different medical access to antibiotics. Our results demonstrate that there is a great diversity of antibiotic resistance (AR) and virulence factor (VF) genetic traits amongst metagenomes in general. In the human gut there are less AR and VF genetic traits than in more versatile environments, yet the correlations between the latter determinants are still strong, advocating that in the human gut microbiome, there appears to be co-selection of these traits, remaining well established and long lasting in the foregoing host’s microbiome. In the USA human gut metagenomes there are a few examples of AR determinants per VF accumulation, suggesting a possible consequence of antibiotic consumption abuse. In Malawi, a very poor African country, where there is a high prevalence of unattended antibiotic consumption, the correlation between AR determinants and VFs is very strong, as opposed to the scenario portrayed by the metagenomes pertaining to Amerindians (native populations of the Venezuelan Amazon) where there is neither reports of pharmaceutical-grade antibiotics consumption nor correlation at all, thus allowing us to link this effect to antibiotic exposure. Furthermore, the best correlations gathered between AR and VF protein sub-families amidst both metagenomic cohorts relate to the bacterial cell envelope, namely multidrug efflux pump components (AR determinants), along with secretion systems, adhesion proteins and iron-acquisition systems (VFs), most of which are known to be encoded within mobile genetic elements.
Arumugam, Manimozhiyan [Verfasser]. "Comparative metagenomic analysis of the human intestinal microbiota / vorgelegt von Manimozhiyan Arumugam". 2010. http://d-nb.info/1011307758/34.
Texto completoFaller, Lina Luise. "Comparative metagenomics to identify functional signatures in the human microbiome". Thesis, 2014. https://hdl.handle.net/2144/14310.
Texto completo邱致閔. "Identifying human microflora and constructing bacterial disease risk evaluation models using Metagenomics analysis platform". Thesis, 2014. http://ndltd.ncl.edu.tw/handle/m3tz8p.
Texto completo國立交通大學
生物資訊及系統生物研究所
102
The human body plays host to a vast array of bacteria which are harmful or beneficial. Next generation sequencing technology have increased its accuracy in identifying bacteria. This work develops a novel platform for Metagenomics analysis, bacterial disease risk evaluation model construction and microbiome characterization in human using high-throughput 16S rRNA sequencing. A database that recorded the bacteria 16s rRNA sequences from literature and public database was constructed, along with quality filtering, chimeric sequence detection, sequence clustering and assigning the taxonomy of the sequenced 16S rRNA sequences. A bacteria disease risk model for seven diseases was constructed based on 174 samples and 78 bacterial disease risk biomarkers. Applicability of the proposed platform is demonstrated by collecting the microbiome in human gut of 81 samples and 53 samples with BMI. For analyzing bacteria related disease, this work expects to collect more bacterial disease biomarkers from human body. Additionally, we design case-control study to finding novel association between bacteria and disease for extending bacterial disease risk evaluation model. The proposed platform provides a relatively easy means of identifying a certain amount of bacteria and evaluating bacterial disease risk based on Taiwanese control group for clinical microbiology applications. Detecting how bacteria inhabit humans and affect their health significantly contributes to develop a diagnosis and treatment method.
Costea, Paul Igor. "Stratification and variation of the human gut microbiota". Doctoral thesis, 2016. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-139649.
Texto completoDie mikrobiellen Gemeinschaften innerhalb des menschlichen Darmtrakts – das menschliche Darm-Mikrobiom - sind wichtig für das Wohlbefinden und die Gesundheit des Wirts. Die Charakterisierung dieses neuen “Organs”, welches aus ähnlich vielen Zellen besteht wie der menschliche Körper, ist in jüngster Zeit durch technologische Fortschritte möglich geworden. Die Metagenomik, die direkte Hochdurchsatz-Sequenzierung mikrobieller DNA, ermöglicht die Aufnahme “genomischer Schnappschüsse” tausender verschiedener, in einem komplexen Ökosystem zusammenlebender Bakterien, ohne dafür auf deren Isolierung und Wachstum angewiesen zu sein. Die Quantifizierung des menschlichen Mikrobioms erlaubt es uns, seine Eigenschaften zu untersuchen und Verbindungen zu Wirtsphysiologie und -krankheiten zu knüpfen. Der Reichtum dieser Informationen ist unerwartet hoch und wahrscheinlich noch immer unterbewertet. Aufgrund der Tatsache, dass der Großteil unserer Ernährung und unseres Medikamentenkonsums unser Mikrobiom, welches wiederum selbst über verschiedene Arten mit unserem Immunsystem interagiert, beeinflusst, wurden viele Mechanismen vorgeschlagen, um die beobachteten Korrelationen zu erklären. Die meisten davon sind jedoch noch nicht vollständig verstanden. Eine offensichtliche Komponente zur Charakterisierung des Mikrobioms und dessen Interaktionen mit dem Wirt ist eine akkurate Quantifizierung seiner genauen Zusammensetzung, womit sowohl die Anwesenheit von bestimmten Bakterien als auch deren Anzahl gemeint ist. Obwohl etablierte Standardprozeduren zur Probenbehandlung, DNA- Extrahierung und Datenanalyse existieren, sind sie nicht immer für metagenomische Studien anwendbar, da sie für isolierte Bakterienkulturen entwickelt worden. Deswegen und auch wegen der Begeisterung, die neuartige Technologien mit sich bringen, nahmen sich die ersten metagenomischen Studien jeweils die Freiheit, ihre eigenen Protokolle und Herangehensweisen zu definieren. Die Metaanalyse dieser Studien zeigte, dass Unterschiede sowohl in der Probenbehandlung als auch in der statistischen Auswertung den Vergleich zwischen Studien sehr schwierig machen. Das wiederum beschneidet unsere Fähigkeit, Entdeckungen zu bestätigen und Daten über Studien hinweg zu kombinieren. Um die zwingend notwendige Standardisierung voranzutreiben haben wir einen umfassenden Vergleich von 21 verschiedenen DNA-Extraktionsmethoden sowie verschiedener weiterer Probenbehandlungen, welche Quantifizierungen beeinflussen, vorgenommen. Wir haben eine Reihe von Kriterien entwickelt, um die Messqualität in Abwesenheit von Mock-Kontrollen zu bestimmen und schlagen anhand dieser Methoden für Probenbeschaffung, DNA-Extraktion und Library- Generierung optimale Verfahren vor. Wenn diese als Standard akzeptiert werden, würde das eine stark verbesserte Vergleichbarkeit zwischen Studien ermöglichen und damit sowohl einen extremen Zuwachs an statistischer Power als auch unserer Fähigkeit, generelle Schlüsse über das Mikrobiom zu ziehen, zur Folge haben. Die meisten metagenomischen Studien teilen ihre Datensätze auf um Vergleiche anzustellen, z.B. zwischen Stuhlproben gesunder und erkrankter Menschen. Eine Vielzahl verschiedener Ansätze, welche wiederum oft mit verschiedenen Datenvorbehandlungen kombiniert werden, wurden vorgeschlagen, um Dissimilarität zwischen Gemeinschaften (Beta-Diversität) zu berechnen. Um metagenomische Daten auf Spezies-, Genus- und höheren Ebenen zu quantifizieren werden üblicherweise reads auf Referenzgenome bestimmter taxonomischer Einheiten aligniert und gezählt. Aufgrund technologieabhängiger Unterschiede in Sequenziertiefe müssen reads normalisiert werden, z.B. indem man alle counts durch die Gesamtanzahl der counts einer Sequenzierung teilt (total sum scaling), oder durch subsampling. Für die Messung der Gemeinschafts(dis)similarität wurden viele Distanzmaße vorgeschlagen. Da es schwierig ist diese Ansätze theoretisch zu vergleichen, haben wir ein biologisch motiviertes Konzept entwickelt, mit dem man Distanzmaße evaluieren kann. Dies unterstreicht die Wichtigkeit der Datentransformation und dessen Einwirkung auf Distanzmaße. Aufbauend auf unserer Erfahrung mit Häufigkeitsabschätzungen und Techniken zur Datenvorbehandlung können wir nun versuchen, grundlegende Eigenschaften mikrobieller Gemeinschaften zu verstehen. 2011 wurde vorgeschlagen, dass sich die Variation auf Genusebene im menschlichen Darm auf drei grundlegende Typen beschränkt, welche Enterotypen getauft wurden. Diese wurden in Datensätzen verschiedener Länder als unabhängig von Herkunft, Alter und anderer Wirtseigenschaften beschrieben. Die Enterotypen sind durch einen Cluster-Ansatz als „dicht besiedelte Bereiche in einem multidimensionalen Raum der Gemeinschaftszusammensetzung“ definiert und wurden als grundlegende Stratifikatoren für die menschlichen Population vorgeschlagen. Spätere Studien, welche dieses Konzept auf andere Datensätze anwandten, erhoben Zweifel bezüglich der optimalen Anzahl an Clustern und an der generellen Robustheit des Ansatzes. Dies leitete erneut eine langanhaltende Debate über die Existenz von Strukturen und die besten Wege, diese zu bestimmen und einzufangen, ein. Hier überdenken wir, in Anbetracht der stark gestiegenen Anzahl an verfügbaren Daten, das Enterotypen-Konzept. Wir schlagen ein überarbeitetes Konzept vor, in welchem die verschiedenen Enterotypen als schwache Attraktoren im multidimensionalen Raum verstanden werden und implementieren einen Ansatz zur Berechnung des Attraktors, der dem Datensatz am ähnlichsten ist. Dafür trainieren wir einen Klassifizierer auf einen Referenz- Datensatz, um neue Datensätze zuzuordnen. Damit ist Enterotypisierung nicht mehr datensatzabhängig und der Effekt von sampling bias ist minimiert. Indem wir ein Modell nutzen für das wir die Existenz dreier Enterotypen (definiert durch die selben Genera wie ursprünglich postuliert) annehmen, zeigen wir die Relevanz dieser Stratifikation und schlagen es in einem klinischen Zusammenhang als potentiellen Marker für Krankheitsfortschritt vor. Außerdem glauben wir, dass diese Attraktoren verschiedene Regeln mikrobieller Zusammensetzung widerspiegeln und schlagen vor, sie bei der Analyse von mikrobiellen Daten zu berücksichtigen. Während Enterotypen Struktur in der Gemeinschaft auf Genusebene beschreiben, kann metagenomische Sequenzierung prinzipiell Auflösung auf Nukleotidebene erreichen, womit single nucleotide polymorphisms (SNPs) und andere genomische Variationen im Darm- Mikrobiom identifiziert werden können. Analysemethoden für dieses Auflösungsniveau wurden erst kürzlich entwickelt und bis heute wurden diese erst wenig erforscht. Wir zeigen, dass die Landschaft an genomischer Variation von SNPs in einer großen, multinationalen Kohorte sogar über die Speziesebene hinaus geht und hochgradig strukturiert ist, was das Vorkommen klar abgrenzbarer Subspezies unter Darmmikroben suggeriert. In mehreren Fällen zeigen diese Subspezies geographische Stratifikation, wobei einige Subspezies nur in chinesischen Populationen vorkommen. Im Allgemein zeigen Sie jedoch nur eine geringfügige Beschränkung der Dispersion und sind in der Mehrzahl der Populationen vorhanden. Innerhalb eines Individuums dominiert häufig eine bestimmte Subspezies, nur selten dominieren verschieden gemeinsam im gleichen Ökosystem. Eine Analyse von Zeitreihenexperimenten deutet darauf hin, dass die dominante Subspezies über Zeiträume von mehr als drei Jahren stabil bleibt. Wenn man ihre funktionalen Eigenschaften untersucht findet man viele Unterschiede, von denen bestimmte relevant für den Wirt erscheinen. Zum Beispiel identifizieren wir eine Subspezies von E. rectale, welcher das Flagellum-Operon fehlt, die signifikant assoziiert ist mit geringerem BMI und geringerer Insulinresistenz ihres Wirts; sie korreliert zudem mit höherer mikrobieller Diversität. Diese Assoziationen konnten auf Speziesebene nicht gesehen werden (auf der mehrere Subspezies überlagert sind), was die Wichtigkeit dieser erhöhten Auflösung für ein umfassenderes Verständnis mikrobieller Interaktionen innerhalb des Mikrobioms und mit dem Wirt illustriert. Zusammenfassend bieten unsere Ergebnisse eine präzise Grundlage für vergleichende Metagenomik des menschlichen Darms, einschließlich Empfehlungen über experimentelles Sampling und statistische Analysen. Weiterhin verfeinern wir das Konzept der Enterotypen- Stratifikation in Gemeinschaften, entwickeln referenzbasierte Ansätze für Enterotypen- Zuordnung und bieten überzeugende Beweise für ihre Relevanz. Indem wir die volle Auflösung metagenomischer Sequenzierungen nutzen entdecken wir eine Landschaft hochgradig strukturierter genomischer Variation unterhalb der Speziesebene und identifizieren gemeinsame Subspezies des menschlichen Darm-Mikrobioms. Durch die Entwicklung dieser hochpräzisen metagenomischen Untersuchungsansätze tragen wir zu einem verbesserten
Byrd, Allyson Lindsay. "Bacterial strain-tracking across the human skin landscape in health and disease". Thesis, 2017. https://hdl.handle.net/2144/21963.
Texto completo2018-03-24T00:00:00Z
Gomes, Carla Filipa Norte. "Analysis of the microbiome of human stool samples : approaching colorectal cancer diagnosis". Master's thesis, 2018. http://hdl.handle.net/10773/25411.
Texto completoDo ponto de vista histológico, o cancro coloretal (CCR) reside na proliferação anormal de células epiteliais da mucosa do cólon, progredindo de adenoma a adenocarcinoma. Este cancro continua a ser o terceiro com maior incidência e mortalidade mundialmente. É causado por um acúmulo de mutações genéticas e silenciamento epigenético, para além de outros fatores de risco intrínsecos e extrínsecos. Devido às altas taxas de incidência e mortalidade, têm vindo a ser criadas, implementadas e otimizadas ferramentas de diagnóstico e prevenção. No entanto, continua premente a necessidade de desenvolver ferramentas que forneçam um diagnóstico cada vez mais precoce, rigoroso e sensível. Neste sentido, os objetivos desta dissertação consistiram em (1) desenvolver o estado da arte acerca das ferramentas de diagnóstico de CCR, (2) resumir as aplicações “ômicas” para indentificar biomarcadores microbianos relacionados com CCR e (3) comparar o microbioma de pacientes portugueses com CCR e indivíduos saudáveis. Atualmente, o diagnóstico de CCR tem vindo a ser conduzido por procedimentos mais (e.g., colonoscopia) ou menos (e.g., técnicas de imagem, biomarcadores moleculares) invasivos. Muito recentemente, a procura de biomarcadores microbianos através de ferramentas “ómicas” tem sido uma alternativa, principalmente devido à relevância do microbioma nas homeostase metabólica e fisiológica, assim como no funcionamento do sistema imunitário do hospedeiro. Assim, ao microbioma intestinal tem sido atribuído um papel ativo na evolução do CCR, podendo influenciar ou ser influenciado pela doença. Em particular, a análise metagenómica e metabolómica do microbioma associado a CCR em amostras de fezes tem estimulado a comunidade científica na procura de biomarcadores sensíveis, fidedignos, diferenciais, estáveis e precoces na deteção não invasiva da doença. Contudo, estes avanços carecem de uma representatividade para diversas áreas geográficas, dada o impacto cultural, genético e ambiental na incidência desta doença. Neste sentido, realizou-se a análise do microbioma (com enfoque em Bacteria) em fezes de dois grupos clínicos constituídos por indivíduos Portugueses (pacientes com CCR e indivíduos saudáveis), através da sequenciação do gene 16S rRNA usando Ilumina MiSeq. Este estudo é um contributo para colmatar a lacuna de conhecimento existente sobre o microbioma associado a CCR na população Portuguesa. Apesar da estrutura do microbioma de fezes assumir padrões homogéneos entre indivíduos do mesmo grupo clínico, houve alguma variabilidade na abundância de taxa entre esses grupos e em diferentes estádios do CCR. Por exemplo, maiores abundâncias de Prevotella, Alloprevotella, Sutterella, Desulfovibrio e Olsenella observadas em amostras de CCR podem servir como biomarcadores microbianos. No futuro, o estudo será alargado a amostras populacionais maiores, assim como a outro tipo de amostras humanas e grupos clínicos, no sentido de identificar assinaturas microbianas sensíveis e específicas, que possam traduzir o desenvolvimento de CCR, reduzindo, assim, as taxas de incidência e mortalidade.
Mestrado em Biologia Molecular e Celular