1,721,031 research outputs found
Deciphering the dietary fibre-degrading enzyme system of the human gut bacterium Bacteroides xylanisolvens using transcriptomic, proteomic and mutagenesis approaches
No full textIn humans, the degradation of dietary fibers is a metabolic function undertaken by the intestinal microbiota. This metabolic function favors the homeostasis of the digestive ecosystem and participates in the prevention of several chronic disorders like metabolic diseases. The bacteria able to initiate this process possess complex enzymatic systems that deconstruct polysaccharides into compounds (oligosaccharides, sugars) that serve as energetic substrates to the whole microbial community. Bactereoides xylanisolvens is a prevalent bacterial species in the human gut that has the particularity to degrade both pectins (soluble fibers found in fruits) and xylans (insoluble fibers found in cereals). The type strain XB1A was isolated in our laboratory and was shown to harbor more than 300 genes encoding carbohydrate active enzymes (CAZymes) that are distributed in 74 genomic loci called Polysaccharide Utilization Loci (PUL). Considering the complexity of B. xylanisolvens enzyme system, the pectinolytic and xylanolytic function was studied using transcriptomics (RNAseq), proteomics and directed mutagenesis. The results highlighted the existence of 6 and 2 PULs involved in pectin and xylan degradation, respectively. Our findings highlight the metabolic plasticity of B. xylanisolvens towards non-starch dietary polysaccharides which contributes to its competitive fitness within the human gut ecosystem
Functional study of pectinolytic and xylanolytic systems of Bacteroides xylanisolvens, a prominent human gut symbiont
No full textChez l’homme, la dégradation des fibres alimentaires est une des fonctions principales du microbiote colique. Elles ont de nombreux effets bénéfiques en santé humaine et pourtant les mécanismes microbiens mis en jeu dans leur dégradation restent encore largement méconnus. L’objectif de cette thèse était d’approfondir les connaissances sur la dégradation des polysaccharides pariétaux (hémicelluloses et pectines) par une espèce bactérienne prédominante du côlon de l’homme, Bacteroides xylanisolvens. L’analyse du transcriptome de B. xylanisolvens XB1AT a révélé l’existence de six et deux loci génomiques respectivement dédiés à la dégradation des pectines et des xylanes. Ces loci ou PULs (« Polysaccharide Utilization Loci ») sont connus chez Bacteroides pour coder pour des systèmes enzymatiques spécifiques d’un polysaccharide en particulier. L’analyse des CAZymes (Carbohydrate-Active Enzymes) codées par les PULs « pectinolytiques » a permis de proposer une cible polysaccharidique (homogalacturonane, rhamnogalaturonane de type I et II, arabinane) à cinq des six PULs identifiés. Les deux PULs « xylanolytiques » cibleraient les xylanes de faible complexité. La mutation du gène susC-like dans le PUL 49 et du gène HTCS (Hybrid Two-Component System) dans le PUL 43 a démontré l’importance respective de ces deux loci dans la fonction pectinolytique et xylanolytique de la bactérie. Le mutant HTCS a aussi permis de montrer pour la première fois que deux PUL peuvent être liés au niveau transcriptionnel. En présence de xylane, les données de protéomique ont souligné la surproduction par la bactérie d’une endo-xylanase possédant deux CBMs (Carbohydrate-Binding Modules). Cette enzyme modulaire pourrait être considérée comme un marqueur fonctionnel de la xylanolyse dans l’écosystème microbien intestinal. En conclusion, B. xylanisolvens déploie une machinerie enzymatique qui reflète la complexité des polysaccharides pariétaux de plantes. La plasticité métabolique de B. xylanisolvens vis-à-vis des fibres alimentaires contribue certainement à sa survie et son maintien dans le côlon humain. Des études d’écologie fonctionnelle ciblant la communauté fibrolytique intestinale sont encore nécessaires afin de mieux décrypter l’impact des fibres alimentaires et en particuliers des polysaccharides pariétaux sur le métabolisme microbien intestinal et par conséquent sur la santé humaine.Dietary fiber degradation is a key function of the human gut microbiota. They have many beneficial effects on human health and yet microbial mechanisms involved in their degradation remain largely unknown. The aim of this thesis was to increase our knowledge on the degradation of plant cell wall polysaccharides (hemicelluloses and pectins) by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide. Analysis of the CAZymes (Carbohydrate-Active Enzymes) encoded by the "Pectinolytic" PULs allowed us to propose a polysaccharide target (homogalacturonan, type I and type II rhamnogalaturonane, arabinan) to five of the six identified PULs. The two identified "xylanolytic" PULs would target low complexity xylan. Mutation of the susC-like gene of PUL 49 and of the HTCS gene (Hybrid Two-Component System) of PUL 43 showed the importance of these two loci in pectinolytic and xylanolytic functions of the bacterium, respectively. The HTCS mutant also revealed for the first time that two PULs can be linked at the transcriptional level. With xylan, proteomic data highlighted the overproduction by the bacterium of an endo-xylanase with two CBMs (Carbohydrate-Binding Modules). This modular enzyme could be considered as a functional marker of xylan breakdown in the intestinal microbial ecosystem. In conclusion, B. xylanisolvens harbors an enzymatic machinery that reflects the complexity of plant cell wall polysaccharides. The metabolic plasticity of B. xylanisolvens towards dietary fibers certainly contributes to its fitness in the human gut. Functional and ecological studies targeting the intestinal fibrolytic community are still necessary to better understand the impact of dietary fibers and in particular plant cell wall polysaccharides on the intestinal microbial metabolism and consequently on human health
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Metabolism of flavan-3-ols by the human gut microbiota : unraveling of bacterial species and genes involved
No full textLes flavan-3-ols font partie des polyphénols les plus consommés par l’Homme et sont présents sous la forme de monomères et d’oligomères tels que les procyanidines. La majorité des flavan-3-ols transite vers le côlon où réside le microbiote intestinal. Alors que les voies métaboliques de dégradation des flavan-3-ols par le microbiote sont relativement bien décrites, les microorganismes et les gènes microbiens impliqués dans ces voies sont très peu connus. L’objectif de la thèse était donc d’identifier les microorganismes et les gènes impliqués dans la dégradation des flavan-3-ols et en particulier des procyanidines. A partir de selles humaines de trois individus sains, des approches de culturomique combinées à un criblage de l’activité métabolique des isolats bactériens par HPLC-DAD ont permis d’obtenir quatre souches de l’espèce Eggerthella lenta et une souche de l’espèce Flavonifractor plautii capables de dégrader la (+) catéchine et la (-) épicatéchine. L’activité de ces souches a ensuite été testée sur les procyanidines de type B (DP2 à 4) et A (DP2) et les métabolites générés ont été caractérisés par LC-ESI-MS/MS. Nous avons ainsi montré pour la première fois que E. lenta est capable de dégrader les procyanidines. La réaction catalysée par E. lenta, validée sur les dimères, correspond à l’ouverture du cycle C de l’unité terminale. Par une approche transcriptomique (RNAseq) réalisée chez E. lenta, couplée à l’expression hétérologue des gènes d’intérêt chez Escherichia coli, nous avons mis en évidence deux gènes (fmber1, fmber2) codant deux benzyl ether reductases impliquées dans l’ouverture du cycle C des monomères et un opéron de deux gènes (pber) catalysant cette réaction sur les dimères de procyanidines de type B. Enfin, deux opérons de trois gènes (cadh, ecadh) codant deux complexes enzymatiques impliqués dans la déshydroxylation du cycle B de la (+) catéchine et de la (-) épicatéchine ont aussi été identifiés. En conclusion, les espèces E. lenta et F. plautii, ainsi que les gènes identifiés dans cette étude, constitueront à l’avenir de bons marqueurs du métabolisme microbien des flavan-3-ols chez l’Homme. Ceci permettra à terme de mieux appréhender les effets de la consommation des flavan-3-ols chez les individus en bonne santé ou à risque de maladies chroniques.Flavan-3-ols are among the most consumed polyphenols by humans and are present as monomers and oligomers such as procyanidins. The majority of flavan-3-ols reach the colon where the intestinal microbiota resides. While the metabolic pathways for the degradation of flavan-3-ols by the microbiota are relatively well described, only a few microorganisms and microbial genes involved in these pathways are known. The objective of the thesis was therefore to identify the microorganisms and genes involved in the degradation of flavan-3-ols and in particular procyanidins. From human stools of three healthy individuals, culturomic approaches combined with screening for the metabolic activity of bacterial isolates by HPLC-DAD allowed us to obtain four strains of the species Eggerthella lenta and one strain of the species Flavonifractor plautii degrading (+)-catechin and (-)-epicatechin. The activity of these strains was then tested on B-type (DP2 to 4) and A-type (DP2) procyanidins and the metabolites generated were characterized by LC-ESI-MS / MS. We have thus shown for the first time that E. lenta degrades procyanidins. The reaction catalyzed by E. lenta on dimers (B-type and A type), corresponds to the opening of the C-ring of the terminal unit. By a transcriptomic approach (RNAseq) carried out in E. lenta, coupled with the heterologous expression of the genes of interest in Escherichia coli, we have discovered two genes (fmber1, fmber2) encoding two benzyl ether reductases involved in the opening of the C ring of the monomers and an operon of two genes (pber) catalyzing this reaction on the dimers of type-B procyanidins. Finally, two operons of three genes (cadh, ecadh) encoding two enzymatic complexes involved in the dehydroxylation of the B-ring of (+)-catechin and (-)-epicatechin have also been identified. In conclusion, the species E. lenta and F. plautii, as well as the genes identified in this study, will constitute good markers of the microbial metabolism of flavan-3-ols in humans in the future. This will ultimately allow a better understanding of the effects of the consumption of flavan-3-ols in individuals in good health or at risk of chronic diseases
Métabolisme des fibres et des polyphénols par le microbiote intestinal humain et répercussions santé
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Deciphering the dietary fibre-degrading enzyme system of the human gut bacterium Bacteroides xylanisolvens using transcriptomic, proteomic and mutagenesis approaches
No full textAnimation workshop "The microbiota"International audienceIn humans, the degradation of dietary fibers is a metabolic function undertaken by the intestinal microbiota. This metabolic function favors the homeostasis of the digestive ecosystem and participates in the prevention of several chronic disorders like metabolic diseases. The bacteria able to initiate this process possess complex enzymatic systems that deconstruct polysaccharides into compounds (oligosaccharides, sugars) that serve as energetic substrates to the whole microbial community. Bactereoides xylanisolvens is a prevalent bacterial species in the human gut that has the particularity to degrade both pectins (soluble fibers found in fruits) and xylans (insoluble fibers found in cereals). The type strain XB1A was isolated in our laboratory and was shown to harbor more than 300 genes encoding carbohydrate active enzymes (CAZymes) that are distributed in 74 genomic loci called Polysaccharide Utilization Loci (PUL). Considering the complexity of B. xylanisolvens enzyme system, the pectinolytic and xylanolytic function was studied using transcriptomics (RNAseq), proteomics and directed mutagenesis. The results highlighted the existence of 6 and 2 PULs involved in pectin and xylan degradation, respectively. Our findings highlight the metabolic plasticity of B. xylanisolvens towards non-starch dietary polysaccharides which contributes to its competitive fitness within the human gut ecosystem
Effet de jus de fruits fermentés sur la composition et la fonction du microbiote intestinal, et sur la réponse de l’hôte
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