Fig. 1

Overview of experimental design. This study involved 54 Simmental crossbred beef calves purchased from individual farmers. Initially, the calves were co-housed for 3 days to allow mingling, during which 10 calves were randomly selected and marked. Subsequently, they underwent a 40-h highway transit, followed by a 6-day acclimation period in the facility. Over the 60 days after their arrival, their rectal temperatures and respiratory-related scores were evaluated twice daily. Body weights were assessed on days 46 and 108 post-arrival. Venous blood and nasopharyngeal swab samples were collected from the 10 marked calves at designated time points A, B, and C for high-throughput sequencing and subsequent bioinformatic analyses. The green dot represents the procedure conducted by staff and the blue dot represents the procedure conducted by researchers