Conserved Developmental Trajectories of the Cecal Microbiota of Broiler Chickens: a Field Study

There is great interest in identifying gut microbiota development patterns and underlying assembly rules to help identify strategies to improve broiler health and performance. Population stratification by using community types (clusters) helps to simplify complex ecosystem principles of the intestinal microbiota. This study aimed to identify community types to increase insight in intestinal microbiota variation between broilers and to reveal factors that explain this variation. Ten well-performing poultry flocks on four different farms were followed. In each flock, the cecal content of nine broilers was collected at 7, 14 and 35 days post-hatch. The cecal microbiota composition of 270 broilers was analyzed using 16S ribosomal RNA gene amplicon sequencing. Two robust community types were observed, one of which was dominated by 7-day-old broilers, and one by 35-day-old broilers. Fourteen-day-old broilers were divided across both community types. In broilers of the same age, the cecal microbiota could not be robustly separated into different community types. This is the first study that showed conserved cecal microbiota development trajectories based on different clustering methods between different commercial broiler flocks. In addition to the observed development with age, cecal microbiota variation between broilers was explained by the poultry flock, body weight, and the different feed components. However, those variables could not be disentangled from the influence of the variables farm. These data support the notion of a conserved development of cecal microbiota, but further investigation of mechanisms underlying microbiota development and function and effects on broiler performance is needed.