ED Sciences de la Vie et de la Santé
Study of the bacterial microenvironment in the context of gastric carcinogenesis
by Marine JAUVAIN (BoRdeaux Institute of onCology)
The defense will take place at 14h00 - Amphithéatre du Batiment BBS Campus Carreire - Batiment BBS 2, Rue du Dr Hoffmann Martinot 33000 Bordeaux
in front of the jury composed of
- Emilie BESSEDE - Maîtresse de conférences - praticienne hospitalière - Université de Bordeaux - Directeur de these
- Eliette TOUATI - Directrice de recherche - Institut Pasteur - Rapporteur
- Christophe BURUCOA - Professeur des universités - praticien hospitalier - Université de Poitier - Rapporteur
- Tamara MATYSIAK-BUDNIK - Professeure des universités - praticienne hospitalière - Université de Nantes - Examinateur
- Raphaël ENAUD - Maître de conférences - praticien hospitalier - CHU de Bordeaux - Examinateur
Gastric cancer is the 5th leading cause of cancer-related mortality worldwide, and infection by the bacterium Helicobacter pylori being the main risk factor. This bacterium colonizes the stomach in over 90% of patients with gastric cancer. By promoting chronic inflammation and remodeling the gastric epithelium through the induction of epithelial-mesenchymal transition, H. pylori contributes to gastric carcinogenesis. However, only 1% of infected patients develop cancer, as this is a multifactorial disease influenced by environmental factors, including the digestive microbiota. In this context, the potential use of probiotics for gastric cancer prevention represents a promising research avenue. The first focus of this thesis investigates the effects of candidate probiotic strains from the Lactobacillaceae family on gastric carcinogenesis induced by H. pylori. Two strains showed an inhibitory effect on the induction of the epithelial to mesenchymal transition, the emergence of cells with cancer stem cell properties, and inflammation induced by H. pylori. The second focus studies the intratumoral microbiota in gastric cancer. Recent studies have revealed that tumors have a microbiome with characteristics specific to tumor types. Regarding gastric cancer, knowledge remains limited. For this study, 24 tumors from patients with gastric cancer who have a gastrectomy at the Bordeaux University Hospital were collected with two clinical research protocols: FREGAT and MICROGAS. For 16 patients, adjacent non-tumoral tissue was also collected during surgery. After DNA extraction, 16S ribosomal DNA sequencing was performed, and analyses on taxonomic composition, alpha diversity, beta diversity, and predicted metabolic functions were conducted using the QIIME2 bioinformatics pipeline. Sequencing revealed a bacterial presence partially composed of oral flora, commonly found in the gastric microbiota. In some patients, the intratumoral microbiota was largely dominated by H. pylori. The analyses showed significant similarities between the microbiota of tumor and adjacent non-tumoral tissues, though with notable differences in richness and taxonomic composition. Additional analyses were conducted to compare the intratumoral microbiota composition based on the histopathological characteristics of the patients. Specific bacterial signatures were identified for factors such as sex, histological type according to the World Health Organization classification, HER2 status, or the neoadjuvant chemotherapy protocol used. H. pylori positivity also significantly influenced the intratumoral microbiota composition. In conclusion, this thesis demonstrated in its first focus that certain Lactobacillus spp. strains exhibit an inhibitory effect on H. pylori-induced gastric carcinogenesis. The second focus characterized the composition of the intratumoral microbiota in gastric cancer, identifying bacterial signatures associated with specific clinicopathological features.
ED Sciences et environnements
Modeling the effect of sediment bypass on the medium to long-term shoreline evolution
by Elsa DURAND (Environnements et Paléoenvironnements Océaniques et Continentaux)
The defense will take place at 14h00 - Amphithéatre bâtiment B18 Bâtiment B18 3 Avenue du Dr Albert Schweitzer 33600 Pessac
in front of the jury composed of
- Bruno CASTELLE - Professeur des universités - UMR CNRS EPOC/Université de Bordeaux - Directeur de these
- Marissa YATES - Chargée de recherche - Ecole des Ponts / Laboratoire d'Hydraulique Saint-Venant - Rapporteur
- Eric BARTHéLéMY - Professeur des universités - LEGI - UMR 5519/Grenoble INP/ENSE3 - Rapporteur
- Stéphane ABADIE - Professeur des universités - SIAME/UPPA - Examinateur
- Albert FALQUéS - Professeur des universités - UPC Universitat Politècnica de Catalunya - Examinateur
- Déborah IDIER - Ingénieure - BRGM - CoDirecteur de these
Under the effect of wave-induced currents, sand can be transported around natural or artificial rocky obstacles transverse to the beach through a process called sediment bypassing. This phenomenon plays a key role in beach evolution, particularly in embayed beaches, which are delimited by two rocky obstacles and represent half of the world's beaches. However, sediment bypassing is often neglected or partially included in shoreline evolution models. The aim of this thesis is to extend the applicability of the reduced-complexity model LX-Shore by implementing a parametrization of sediment bypassing. The new version of the model, which integrates the impact of subaqueous bypassing around obstacles, has been tested on an idealised embayed beach subject to various wave incidence conditions. The results show that accounting for bypassing significantly influences embayed beach planform and shoreline spatial variability, in terms of rotation, curvature, and maximum erosion. Applications to real beaches featuring rocky groynes in Denmark and Fréjus (France) or a longitudinal defense structure in Lacanau (France) have provided insights into the influence of bypassing across different timescales: event-scale, annual-scale, and multi-decadal-scale under the effect of sea level rise. By integrating for the first time a generic parametrization of sediment bypassing into a reduced-complexity model, this work contributes to improving the understanding and modeling of shoreline evolution in the presence of rocky obstacles, offering new perspectives for coastal management.
Would organic agriculture expansion and reduced animal-based foods consumption in Europe be compatible? A global analysis based on nitrogen cycling, land-use and greenhouse gas emissions
by Noélie BORGHINO (ISPA - Interaction Sol-Plante-Atmosphère)
The defense will take place at 9h30 - Salla de conférence ISPA Centre INRAE Nouvelle Aquitaine - Bordeaux Batiment C1 (ISPA) 71 avenue Édouard Bourlaux CS 20032 33882 Villenave d'Ornon
in front of the jury composed of
- Thomas NESME - Professeur - INRAE - Directeur de these
- Chantal LE MOUEL - Directrice de recherche - INRAE - Directeur de these
- Patrick MEYFROIDT - Professor - Université Catholique de Louvains - Rapporteur
- Pierre GERBER - Professor - Université de Wageningen / Banque Mondiale - Rapporteur
- Souhil HARCHAOUI - Chargé de recherche - INRAE - Examinateur
- Marie-Helene JEUFFROY - Directrice de recherche - INRAE - Examinateur
- Elin ROOS - Senior Lecturer - Swedish University of Agricultural Sciences - Examinateur
Future climate related risks depend on our ability to curb greenhouse gas (GHG) emissions, which require a profound food system change. Organic farming and dietary shift towards more plant-based diets are often seen as promising ways to mitigate GHG emissions. They are both promoted by the European Union (EU), which aims for climate neutrality by 2050. However, the expansion of organic farming is controversial, as it could lead to land use changes – and associated CO2 emissions – to compensate for lower productivity. Therefore, the EU's goal of dedicating 25% of its agricultural land to organic farming by 2030 has been criticized, particularly because the globalization of agricultural trade could lead to emissions being shifted to other regions. Furthermore, the interactions between dietary changes and the development of organic farming have not been sufficiently explored. A reduction in livestock, driven by a lower demand for animal products, might relax agricultural land demand for producing feed and compensate for higher land requirement of organic systems. However, the reduced availability of manure could negatively affect nitrogen (N) inputs to organic crops and challenge organic systems productivity. This could undermine the GHG mitigation potential of both strategies, especially in the case of a drastic reduction in animal product consumption, as in vegan diets. Therefore, the aim of this thesis is to assess the combined effects of these two levers in Europe on land use and GHG emissions, considering the effects related to the N cycle. We first reviewed studies that explored the effects of organic farming expansion using a modeling approach. We showed that considering N availability feedback on crops yields exacerbates the anticipated drop in agricultural production. Next, we used the GlobAgri model, which computes croplands and permanent grasslands requirements at the scale of large global regions in 2050, to simulate the adoption of vegan diets in Europe, with or without maintaining livestock for export. Our results show that the impacts on croplands N balance depend on the relative adjustment of two compensatory factors: the decrease in manure availability, and the decrease in the land required for producing feed. Finally, we simulated scenarios combining dietary changes and widespread adoption of organic practices by coupling two models: i) GOANIM, which simulates N balances of organic cropland, yields, and animal densities, and ii) an adapted version of GlobAgri. We found that a higher share of organically managed land would lead to an increase in European cropland demand, due to lower crop yields and changes in crop rotations. This increase would allow Europe to maintain its market shares, preventing emissions to increases in the rest of the world. In a scenario without dietary changes, 25% organic cropland would increase the domestic GHG balance by 10%. In scenarios combining more plant-based diets with more disruptive organic practices, emissions from land-use changes would be offset by reduced land requirements and livestock-related emissions, up to 50% organic cropland. Beyond that, the land demand to maintain export shares would be too high. Overall, our work contributes to include complex interactions between crops, livestock, N cycle, global trade, and GHG emissions in large-scale models. It provides suggestions for effectively combining the expansion of organic farming with dietary shifts towards more plant-based diets.