Assessment of endogenous and exogenous microbiotas of patients with chronic respiratory disease

• Main Author: Vandenborght, Louise-Eva
• Other Authors: Centre de recherche Cardio-Thoracique de Bordeaux Bordeaux (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux, Laurence Delhaes, Stéphanie Ferreira
• Format: Doctoral or Postdoctoral Thesis
• Language: French
• Published: HAL CCSD 2019
• Subjects: Microbiota; Mycobiota; Deep-Sequencing; Asthma; Indoor air; Cystic fibrosis; Microbiote; Mycobiote; Séquençage haut-Débit; Asthme; Air intérieur; Mucoviscidose; [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology; North Pole
• Online Access: https://theses.hal.science/tel-03112231; https://theses.hal.science/tel-03112231/document; https://theses.hal.science/tel-03112231/file/VANDENBORGHT_LOUISE-EVA_2019.pdf

The microorganisms, some of which preceded us billions of years ago, have been identified from the North Pole to the bottom of the ocean until in the atmosphere. The advent of High Throughput Sequencing (HTS) technologies has facilitated the discovery and study of these microbial communities, including the human body. Thus, the human body appears to be composed of ten times more microorganisms than its own cells. Notably, the intestinal microbiota is one of the most investigated; it is composed of a significant biomass. In contrast, studies on the pulmonary microbiota are only in their early stages, particularly in the context of chronic respiratory diseases (CRD). While until recently lungs were considered as sterile organs, they are now found to be composed of a poly-microbial community of bacteria, viruses, phages and fungi. In the case of CRD, such as asthma and cystic fibrosis studied in this PhD work, the composition of the pulmonary microbiota determined by NGS appears to correlate with the clinical course of the patients.In cystic fibrosis (the most common genetic disease in the Caucasian population) and asthma (a multifactorial disease attributed to environmental factors associated with a genetic predisposition which knows a constantly increasing prevalence), changes in abundance and diversity (known as dysbiosis) of bacterial communities (endogenous microbiota) are well documented. However, the study of endogenous mycobiota (fungal community that resides into the lungs) remains much less investigated. Indeed, it presents methodological challenges inherent to its very low biomass, but also to the structure of fungi wall.In addition, very few information exits on the relationship between the endogenous pulmonary microbiota of patients and the corresponding indoor environment (or exogenous microbiota), whereas this specific fungal exposure represents a known risk factor for the development of a CRD. The study of such microbial exposome also presents methodological challenges, in terms of sampling and ...