Supplementary file 1 - classification system

Results of diagnostics on respiratory tract samples from 25 animals, derived from 3 different veal calf herds. Calves were either sampled immediately before or after the first metaphylactic treatment for respiratory disease was initiated (treatment initiation, wk1), or immediately after treatment was ended. Metagenomic sequencing was performed on a pooled nBAL sample of 5 animals from each herd.