Abstract
The increase in the emergence of zoonoses due to human activities is prompting us to refocus infectious diseases at the center of global concerns, by adopting a "One Health" approach. The integration of community ecology with epidemiology enables us to take into account all the ecological processes that influence both multiple hosts and multiple micro-organisms. By exploring the relationships between the latter in the transmission of zoonotic diseases, we could open up new perspectives for better prevention of zoonotic danger. Given the zoonotic risk posed by small mammals and the threat to their diversity posed by anthropization, we need to find new ways of managing these communities to limit the circulation of pathogens. In the long term, this would make it possible to establish strategies that benefit both biodiversity and health.The aims of this thesis were to understand the complex links between small mammal biodiversity, their microbiota and pathogens along an anthropization gradient. This included: i) monitoring the zoonotic hazard associated with small mammals in France, ii) understanding the links between small mammal biodiversity and the prevalence of multiple pathogens, in different environmental and management contexts, iii) examining the relationship between small mammal biodiversity and their microbiota, iv) analyzing the interactions between microbiota and pathogens.To this end, we sampled small mammal communities along a forest anthropization gradient, then performed serological and molecular analyses to detect and characterize zoonotic agents and gut microbiota. We then carried out statistical analyses and epidemiological modelling to understand the associations between zoonotic pathogens and microbiota, and their impact on the link between biodiversity and zoonotic danger.Along a gradient of anthropization, we have identified the presence of multiple pathogens in various rodent species, representing a real risk to public health. Anthropization has altered the composition and diversity of small mammal communities, as well as their microbiota. These changes have affected the relationship between biodiversity and pathogens. We found that unbalanced small mammal communities, with a higher abundance of competent species, were associated with an increased prevalence of pathogens. However, community management strategies such as deratting could have a counter-intuitive impact by reducing small mammal diversity and increasing pathogen circulation.The ecological mechanisms underlying microbiota composition varied according to species type, and seemed to play a crucial role in their resistance to anthropogenic disturbance. Furthermore, interactions between pathogenic and commensal microorganisms suggest that a host's susceptibility to a pathogen may be linked to the composition of its microbiota. With these results, new hypotheses emerge concerning the role of the microbiota in the competence of the host species and its susceptibility to pathogens.Thus, disturbances induced by various anthropogenic pressures can cause an imbalance in communities, which can alter the overall interactions between multiple hosts and micro-organisms, and consequently increase the circulation of pathogens. This underscores the importance of exploring new methods and approaches for a better understanding of these complex relationships between biodiversity, microbiota and public health, in particular by applying an integrated health approach.