When analysing microbiota composition in the chicken caecum, central is to realise differences in the structure of microbiota in chickens during first weeks of life and adult hens. Though it is impossible to ignore commercial production, caecal microbiota of broilers cannot be considered as characteristic for Gallus gallus. Much longer time than that used for broiler production is necessary for establishment of adult type of caecal microbiota in chicken in commercial production (for details see here). Newly hatched chicks can be colonised by adult type microbiota from the very first days of life (see for example here, here or here). To define the most appropriate bacterial species and isolates for the colonisation of newly hatched chicks and thus replace missing hen in commercial production, it is useful to compare microbiota of a wide spectrum of different chickens (see here) such as egg layers from commercial production, egg layers from non-commercial private owners (backyard chikor even from different lines of chickens exhibited in Zoopark Vyskov.