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Replication Data for: Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening
No full text16S rRNA metabarcoding from FIT positive samples (raw sequence reads
Structure et diversité trophique des producteurs primaires picoeucaryotes dans l'océan global
No full textPrimary production is the synthesis of organic matter out of inorganic molecules, and in most ecosystems is achieved through photosynthesis. Eukaryotic microbial phototrophs and mixotrophs are main contributors to primary production in the global oligotrophic ocean, supporting processes of energy and biomass trophic transfer at a planetary scale. Despite the ecological value of these organisms, their wide taxonomic and functional diversity remains largely unknown. In this thesis, we use different types of molecular data obtained from the Tara Oceans circumglobal expedition to assess the composition and trophic diversity of picoeukaryotic primary producers in the oligotrophic ocean. In the first part of the thesis, we compare metagenomic and metabarcoding data to assess the evolutionary diversity and relative abundance of picophototrophic organisms. We identified phototrophic bacteria as three-fold more abundant and significantly less phylogenetically diverse than phototrophic picoeukayrotes. Prymnesiophyceae, Mamiellophyceae, Pelagophyceae and Dictiochophyceae appeared as the dominant groups of phototrophic picoeukaryotes in terms of relative richness and abundance. In the fourth chapter, we describe a predictive model to quantify the abundance of trophic groups in metagenomic samples. This taxonomy-free approach revealed the dominance of photo-trophic organisms across all ocean basins, while the contribution of phagomixo- and phago-trophs oscillated around 25% of the relative abundance in most samples. In the last study included in this thesis we assess the distribution of a collection of single-cell amplified genomes across all Tara Oceans samples. Our results argue that single-cell sequencing technique has the potential to recover the genome of dominant protists in the global oligotrophic ocean with a relatively low sampling effort. Overall, this work describes a number of approaches based on molecular data for the assessment of primary producers distribution and diversity in marine environments.La production primaire est la synthèse de matière organique à partir de molécules inorganiques et, dans la plupart des écosystèmes, elle est réalisée à travers de la photosynthèse. Les microbiens eucaryotes phototrophes et mixotrophes sont les principaux contributeurs à la production primaire dans l'océan oligotrophe global, soutenant les processus de transfert trophique d'énergie et de biomasse à l'échelle planétaire. Malgré la valeur écologique de ces organismes, leur grande diversité taxonomique et fonctionnelle reste largement inconnue. Dans cette thèse, nous utilisons différents types de données moléculaires obtenues à partir de l'expédition circumglobale de Tara Oceans pour évaluer la composition et la diversité trophique des producteurs primaires picoeucaryotes dans l'océan oligotrophique. Dans la première partie de la thèse, nous comparons les données métagénomiques et de métabarcodage pour évaluer la diversité évolutive et l'abondance relative des organismes picophototrophes. Nous avons identifié les bactéries phototrophes comme trois fois plus abondantes et significativement moins phylogénétiquement diversifiées que les picoeukayrotes phototrophes. Les Prymnesiophyceae, Mamiellophyceae, Pelagophyceae et Dictiochophyceae sont apparus comme les groupes dominants de picoeucaryotes phototrophes en termes de richesse relative et d'abondance. Dans le quatrième chapitre, nous décrivons un modèle prédictif pour quantifier l'abondance des groupes trophiques dans les échantillons métagénomiques. Cette approche, qui ne dépend pas de la attribution taxonomique, a révélé la dominance des organismes phototrophes dans tous les bassins océaniques, tandis que la contribution des phagomixo- et phago- trophées oscillait autour de 25% de l'abondance relative dans la plupart des échantillons. Dans la dernière étude incluse dans cette thèse, nous évaluons la distribution d'une collection de single-cell amplified genomes dans les échantillons de Tara Oceans. Nos résultats soutiennent que la technique de séquençage unicellulaire a le potentiel de récupérer le génome des protistes dominants dans l'océan oligotrophique global avec un effort d'échantillonnage relativement modeste. Dans l'ensemble, ce travail décrit un certain nombre d'approches basées sur des données moléculaires pour évaluer la distribution et la diversité des producteurs primaires dans les environnements marins
Exploring the Ocean's biological dark matter using simple eukaryotik cell genomics and transcriptomics applied to world meta-omics datasets
No full textMemoria de tesis doctoral presentada por Laura Rubinat Ripoll para obtener el título de Docteur en la Spécialité Écologie por la Sorbonne Université, realizada bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC), del Dr. Colomban de Vargas y el Dr. Olivier Jaillon.-- 181 pages, figures, tables[EN] Primary production is the synthesis of organic matter out of inorganic molecules, and in most ecosystems is achieved through photosynthesis. Eukaryotic microbial phototrophs and mixotrophs are main contributors to primary production in the global oligotrophic ocean, supporting processes of energy and biomass trophic transfer at a planetary scale. Despite the ecological value of these organisms, their wide taxonomic and functional diversity remains largely unknown. In this thesis, we use different types of molecular data obtained from the Tara Oceans circumglobal expedition to assess the composition and trophic diversity of picoeukaryotic primary producers in the oligotrophic ocean. In the first part of the thesis, we compare metagenomic and metabarcoding data to assess the evolutionary diversity and relative abundance of picophototrophic organisms. We identified phototrophic bacteria as three-fold more abundant and significantly less phylogenetically diverse than phototrophic picoeukayrotes. Prymnesiophyceae, Mamiellophyceae, Pelagophyceae and Dictiochophyceae appeared as the dominant groups of phototrophic picoeukaryotes in terms of relative richness and abundance. In the fourth chapter, we describe a predictive model to quantify the abundance of trophic groups in metagenomic samples. This taxonomy-free approach revealed the dominance of photo-trophic organisms across all ocean basins, while the contribution of phagomixo- and phago-trophs oscillated around 25% of the relative abundance in most samples. In the last study included in this thesis we assess the distribution of a collection of single-cell amplified genomes across all Tara Oceans samples. Our results argue that single-cell sequencing technique has the potential to recover the genome of dominant protists in the global oligotrophic ocean with a relatively low sampling effort. Overall, this work describes a number of approaches based on molecular data for the assessment of primary producers distribution and diversity in marine environments[FR] La production primaire est la synthèse de matière organique à partir de molécules inorganiques et, dans la plupart des écosystèmes, elle est réalisée à travers de la photosynthèse. Les microbiens eucaryotes phototrophes et mixotrophes sont les principaux contributeurs à la production primaire dans l’océan oligotrophe global, soutenant les
processus de transfert trophique d’énergie et de biomasse à l’échelle planétaire. [...
Global comparative analysis of prokaryotic and eukaryotic diversity contributing to oceanic photosynthesis using data from Tara Oceans and Malaspina expeditions
No full textTrabajo final presentado por Laura Rubinat Ripoll para un Máster de la Universitat Pompeu Fabra (UPF), realizado bajo la dirección del Dr. Ramiro Logares del Institut de Ciències del Mar (ICM-CSIC)Peer Reviewe
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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