Decoding the dynamics of calves’ respiratory and gut microbiota: exploring stability, resistance, and individual patterns 

To uncover the intricate relationship between the microbiota, host, and environment in early life, we monitored the temporal dynamics of the nasal and gut microbiota in 30 veal calves over their first five months. Our findings reveal that microbiota stability and individuality are specific to each body site. Notably, the fecal microbiota demonstrated greater diversity, bacterial biomass, stability, and homogeneity as the animals matured. In contrast, nasal microbiota exhibited a skewed structure and higher turnover, likely driven by microbial immigration and mucociliary clearance. Weather, diet, and antibiotics were associated with both microbiotas, alongside host cytokine profiles. Rectal temperature significantly shifted the microbiota structure in both sites, more than diarrhea or respiratory scores. As calves aged, synchronized microbiota dynamics across body sites emerged. This study presents a detailed view of microbial temporal patterns and their connection to the host and environment, offering valuable insights for improving management during critical development periods.