Chickens in commercial production are exposed to environment which differs from their natural environment. Moreover, due to absence of contact between chicks and hen, environment is the only source of microbiota for chickens in commercial production during their first days of life. However, which matrices from the environment is the most important for chicken health? Are these remains of egg shells and other biological material in hatcheries? Is this drinking water? Or feed? Or fresh bedding before chicken placement on farm? Or is this bedding and developing litter? What microbiota is present air of animal houses? Is it possible to influence composition of environmental microbiota by distribution of “environmental probiotics”? Although there are a few studies of this type, knowledge in this area is underdeveloped and we are also making only the first steps to understand ecology and circulation of bacteria in the whole chicken production system.