In vivo expression of chicken gut anaerobes identifies carbohydrate or amino acid utilisers, motile bacteria or type VI secretion system expressing bacteria

One of the possibilities how to decipher the role of gut microbiota in chicken resistance to enteric pathogens is to gradually characterise gene expression of individual gut microbiota members when colonising the chicken caecum.Knowledge of the expression of metabolic pathways like carbohydrate or amino acid fermentation, motility or type VI secretion system is thus important for the gradual understanding of the role of individual gut microbiota members and subsequently of the whole community.