The Influence of the Microbiota on T Cell Development

T cell development occurs in the thymus and is a complex and well-regulated process. Errors during this process can lead to immunodeficiencies and autoimmunity. This project will also look at recent thymic emigrants (RTEs). RTEs are the most immature subset and have been shown to have distinct phenotypes compared to mature naïve T cells (MNTs), including being more prone to differentiate into peripherally induced regulatory T cells, which makes the cells interesting in the context of things such as autoimmunity. Previous research has suggested that the microbiota, particularly the gut microbiota, is able to influence T cell development in the thymus, including shaping the T cell receptor (TCR) repertoire in thymocytes. The impact of the microbiota on T cell development, however, still remains an understudied area of research. There has also been no published data exploring the effects of the microbiota on RTE phenotypes and functions. In this project, I aimed to explore the influence of the microbiota on T cell development in the thymus and the influence of the microbiota on RTE phenotypes and functions. In this project, I also aimed to explore the effect of exposure to the maternal microbiota on thymocyte development and RTE phenotypes. This project used the RAG2:GFP model for the identification of RTEs, in which RTEs are identified as GFP positive peripheral T cells. To explore the effects of the microbiota thymocyte development and RTEs, this project also used mice, including the RAG2:GFP model, which had increasingly complex microbiotas; germ free (GF, with no microbiota), Oligo-Mouse-Microbiota (OMM12, with a gut microbiota which consists of 12 well defined bacterial species), and Specific pathogen free (SPF, with complex undefined microbiotas). To study the effects of the maternal microbiota, an in vivo colonisation system with auxotrophic E. coli HA107 was used. In this project, I showed that the microbiota can impact several aspects of thymocyte development, which had not been previously identified, including RAG2 protein expression and thymocyte proliferation, which are associated with TCR diversity. I found that RTE phenotypes, including migration and response to antigen stimulation, were not influenced by the colonisation state of the mouse. Exposure to the maternal microbiota in utero was not sufficient to rescue some aspect of thymocyte development, which was disrupted in GF mice, including RAG2 expression, but appeared to rescue and even promote other aspects, such as thymic FOXP3 expression. Overall, in this project, I identified novel ways in which the microbiota influences T cell development. Identifying mechanisms by which the microbiota is able to impact T cell development may uncover novel therapeutic targets for conditions such as autoimmunity and immunodeficiencies.