Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

Background: The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large phenotypic databases available for wild and non-model species, these data will provide an unprecedented opportunity to "genomicise" ecological model organisms and establish the genetic basis of quantitative traits in natural populations

Complex interactions between gut microbiota and the mitochondria contribute to the pathogenesis of autoimmune skin diseases

Autoimmune diseases are thought to be caused by complex interactions of genetic and environmental factors. Shifts in gut microbial communities and the reduction in their diversity are found in a variety of diseases, including autoimmune diseases. Bullous pemphigoid is the most common autoimmune blistering skin disease (AIBD), which is mediated by autoantibodies targeting type XVII collagen. To the best of our knowledge, no experimental studies have been conducted to elucidate the impact of gut microbiota in AIBD. Therefore, we first induced a well-established experimental epidermolysis bullosa acquisita (EBA) in germ-free mice. Germfree C57BL/6Tac mice, which received pathogenic IgG against type VII collagen exhibited significantly milder disease severity compared to the conventionally housed C57BL/6Tac mice (padj. T), compared to wild-type C57BL/6J (B6) mice. In the human equivalent gene, MT-ATP8, polymorphisms are associated with bullous pemphigoid in a German cohort. In line with this human study, B6-mtFVB mice demonstrated significantly less skin inflammation than B6 mice when experimental EBA was induced (P < 0.05). To further confirm a potential interaction of the gut microbiota and AIBD, shotgun metagenomics of cecum content, RNA-seq of cecum epithelium samples, and untargeted metabolomics of liver samples of B6-mtFVB and B6 mice were performed. Integrated analysis of shotgun metagenomics and untargeted metabolomics analysis is currently being conducted to identify the gut microbiome derived metabolites that may modulate host immune cell response. Additionally, we evaluated the immune cell metabolism in CD4 + T cells, a pivotal player in the pathogenesis of skin inflammation in the experimental EBA. CD4 + T cells from B6-mtFVB mice demonstrated a higher ratio of glycolysis to oxidative phosphorylation than those from B6 mice (P = 0.0008). This change may further modulate CD4 + T cell function, as we observed less cellular proliferation capacity upon immunological stress induced by anti-CD3 and anti-CD28 antibodies (P < 0.05) and less proinflammatory cytokine IL-17 production in CD4 + T cells from B6-mtFVB mice than B6 mice (P < 0.01). We also evaluated gut permeability via gene expression of tight junction proteins (Claudin-2, Claudin-15, Occludin and ZO-1). Expression levels of these genes were reduced in small intestine, cecum and colon samples of B6-mtFVB compared to those of B6 mice. Our findings show 1) experimental evidence demonstrating the importance of the gut microbiota in the pathogenesis of AIBD, and that 2) a single polymorphism in the mitochondrial genome impacts the composition of gut microbiota, host metabolites and immune cell metabolism, which further modulate disease severity in autoimmune skin inflammation in mice. To explore the link between gut microbiota and immune cell interaction, we plan to identify gut microbiota-derived metabolites and evaluate their modulatory effect on immune cells contributing to autoimmune skin inflammation in vitro and in germ-free B6-mtFVB and B6 mice which are currently being generated