The calf holobiont under challenge: longitudinal microbiota-pathogen dynamics and respiratory health.

The bovine respiratory disease complex (BRDC) is a major health and welfare challenge driven by multifactorial interactions among pathogens, the host, the microbiota, and environmental pressures, reflecting the holobiont nature of the calf. Many implicated bacterial pathogens are also respiratory tract commensals, complicating diagnosis, risk assessment, and prevention. Although the potential association of the respiratory and gut microbiotas in BRDC is only beginning to be recognized, their integrated effects have not yet been investigated. Here, we dynamically followed the microbiota, pathogen load, and host response in 30 calves over 147 days under commercial rearing conditions. Nearly half developed BRDC, presenting fever, cough, and abnormal lung sounds, with peak symptoms at day 58 after arrival. Notably, the large majority of these were acute cases, with only a small subset experiencing more than one episode. Pathogen detection in the nasal cavity revealed clear temporal dynamics. Mycoplasma bovis and bovine coronavirus (BCoV) showed their highest loads during the first 2 weeks of life. At 1 month, influenza D virus (IDV) and Histophilus somni peaked, and Pasteurella multocida also reached its maximum abundance and persisted thereafter. Mannheimia haemolytica became prominent later, with a marked increase after 2 months. Importantly, M. haemolytica and P. multocida loads correlated with higher BRDC scores, whereas BCoV was associated with diarrhea. Microbiota analysis showed that nasal beta-diversity diverged between groups at the symptomatic window, and that healthy animals exhibited early life fecal diversity and evenness. Respiratory pathobionts such as Pasteurella and Corynebacterium were enriched in diseased calves, whereas potentially protective families (Lachnospiraceae, Oscillospiraceae) were more abundant in healthy ones. Multivariate analyses further showed that antibiotic treatments and short-chain fatty acids, especially propionic, butyric, iso-valeric, and iso-butyric acids, modulated both fecal and nasal microbiota, with consistently stronger effects in diseased animals. Together, these findings indicate that BRDC outcomes are shaped not by pathogen burden alone but by the interplay among respiratory and digestive microbiotas, pathogens, environment, and management factors. Our study highlights the importance of a holobiont perspective that integrates both gut and respiratory microbiotas to better elucidate the complexity of BRDC. Such an inclusive framework may provide new insights into disease mechanisms and inform the development of innovative therapeutic strategies.