CDR3 sequences of germ-free and conventional chickens

Microbial colonisation is paramount to the normal development of the immune system, particularly at mucosal sites. However, the relationships between the microbiome and the adaptive immune repertoire have mostly been explored in rodents and humans. Here, we report a high-throughput sequencing analysis of the chicken TCRβ repertoire and the influences of microbial colonisation on tissue-resident TCRβ+ cells. The results reveal that the microbiome is an important driver of TCRβ diversity in both intestinal tissues and the bursa of Fabricius, but not in the spleen. Of note, public TCRβ sequences (shared across individuals) make a substantial contribution to the repertoire. Additionally, different tissues exhibit biases in terms of their V family and J gene usage, and these effects were influenced by the gut-associated microbiome. TCRβ clonal expansions were identified in both colonised and germ-free birds, but differences between the groups were indicative of an influence of the microbiota..., Tissue samples (spleen, bursa of Fabricius, jejunum, caecum, and colon) were derived from an in vivo study carried out at the infectiology platform PFIE (INRA, Val de Loire) in accordance with the national and international regulations specific to the research facility as part of the Development of Immune Function and Avian Gut Health (DIFAGH) consortium. One group of PA12 white leghorn chickens (n=5) was reared under germ-free conditions, whilst another group (n=5) was reared under conventional specific pathogen-free (SPF) conditions. For the germ-free birds, the eggs were collected immediately after laying and surface sterilized by immersion in 1.5% Divosan Plus VT53 (Johnson Diversey, France) for 5 minutes at room temperature. Subsequently, these eggs were transferred into HEPA-filtered incubator. After 18 days at 37°C, the surface of the eggs was sterilized in 1.25% Divosan for 4 min at 37 °C. After hatching, the temperature of the isolator was maintained at 37.5 °C for 7 days, then..., This is a *.csv file and can be opened with programs such as Microsoft Office Excel. For processing and analysis, we recommend the use of a program such as R studio, as was done during the data analysis described in the publication.