A longitudinal field trial to assess the temporal dynamics of fecal microbiota in milk-fed calves and the impact of antibiotic treatment. dynamics of calf fecal microbiota

Establishment of the microbiota in early life is a critical process for the health of the host. The microbiota is influenced by various physiological traits throughout the life of the host, as well as disruptive elements, such as antibiotic treatment. We studied the dynamics of fecal microbiota in milk-fed calves receiving antibiotic treatment to better understand this process. We analyzed 308 fecal samples from 44 veal calves of three farms during their first six months of life. Calves were followed during the entire fattening period, providing insight into the establishment of the fecal microbiota of milk-fed hosts. We performed a cohort study on three French veal farms (named A, B, and C) located in the region of Brittany, France. Sampling began upon the arrival of batches of new calves in October and November 2015. A batch was defined in the study as a group of calves entering the farm at the same time and reared together until slaughter. Fifteen calves were randomly selected from each farm and sampled by rectal swabbing 7 and 21 days after their arrival. Then, rectal swabs were collected once a month, for five months, until the departure of the batch to the slaughterhouse.Seven rectal swabs were obtained from each calf.