Gut microbiota composition before infection determines the Salmonella super- and low-shedder phenotypes in chicken

Heterogeneity of infection and extreme shedding patterns are common features of animal infectious diseases. The super-shedder host individuals are considered key targets for control strategies. Nevertheless, the mechanisms, dynamics, and patterns of diversity associated with the emergence of super-shedders remain largely unknown. For chicken salmonellosis, we have shown recently that high heterogeneity of infection is observed in isolator, an experimental device allowing to reduce animal-animal cross-contaminations and reinfections. With this device, we suggested that unlike the super-shedders, the low-shedders are able to block the first Salmonella colonization. In the present paper, we demonstrated that (1) chicks either bred in axenic conditions or harbouring depleted gut microbiota are more prone to become super-shedders; (2) it is possible to acquire the super or low-shedder phenotypes through microbiota transfer; (3) the chicks bred in isolator, which will develop the low-shedder phenotype after Salmonella infection, present specific gut microbiota taxonomic features before infection. These observations show the key role of gut microbiota composition in heterogeneity of infection and pave the way of developing predictive biomarkers and protective probiotics.