Impact of bacterial mono-colonization on intestinal and splenic CD4 T cells responses

Intestinal T cells responses are strongly influenced by microbes. In this study we aimed to adress how different microbes and what microbial factors influce intestinal T cells differentiation and subsequent clonal expansion. Paticularly we choose Clostridium ramosum (Cr) as a strong induced of a subest of intestinal Tregs (Rorc+), a medium inducer or Rorc+ Tregs an T1h7 Escherichia coli Nissle (EcN) and a strain that did not impact either o those cell (Pm). In addition, to study the impact of Escherichia coli Nissle (EcN) ploysaccharide K5 capsule on intestinal T cells activation, we used a EcN strain lacking the K5 capsule (kfiCD). At day 21 post-monocolonization we isolated CD4 T cells from monocolonized mice in both intestinal Lamina Propria and spleen and performed single cells RNA and TCR seq. Germ-free mice were monocolonized by oral gavage for 2 weeks with the indicated microbes: C. ramosum (CR), P.magnus (PM), E.coli Nissle (EcN) and EcN mutant kifCD (kif). To assess the transcriptional inductions in colonic and splenic CD4 T cells, we flow-cytometrically sorted CD4 T cells (DAPI- CD19- CD4+ TCRβ+) or for somesamples CD4 (DAPI- CD19- CD4+ TCRβ+ CD44+) from Germ-free mice (GF), CR, PM, EcN wild-type (EcN) and EcN kfiCD (kif) mutant at day 14 post-monocolonization and single cell RNA and TCR seq.