Biology subjects

NOUVEL, X.

Publications and source records attributed to NOUVEL, X..

2 recordsLinked to original sources

bioRxiv2026

Gut and nasal microbiome trajectories shape respiratory disease severity in calves exposed to antibiotic and pathogen challenge

Bovine respiratory disease complex (BRDC) is a multifactorial syndrome resulting from interactions among pathogens, host responses, and environmental stressors. However, substantial variation in disease severity persists among animals exposed to similar infectious challenges. To assess the contribution of the respiratory and gut microbiota to BRDC severity, we experimentally inoculated 28 calves with Mycoplasma bovis, bovine coronavirus (BCoV), and influenza D virus (IDV), with half receiving metaphylactic tilmicosin. Clinical trajectories were classified into mild, moderate, and severe phenotypes using unsupervised clustering of longitudinal health scores. Severe BRDC was associated with higher and more persistent nasal IDV loads, yet pathogen burden alone failed to explain the marked inter-individual variability in clinical outcomes. Tilmicosin-treated calves developed substantially milder disease despite comparable pathogen loads, coinciding with lower systemic inflammation, suggesting that host-pathogen interactions, rather than pathogen replication alone, influenced disease severity. Neither nasal nor faecal microbiota diversity consistently explained BRDC severity. However, calves that later developed severe disease displayed a more homogeneous nasal microbiota before infection, indicating that early microbial community structure may influence susceptibility. In contrast, the strongest disease-associated microbial signatures were observed in the faecal microbiota. Gut antibiotic-induced dysbiosis revealed associations between BRDC severity, specific intestinal bacterial taxa, systemic inflammation, and faecal short-chain fatty acid (SCFA) profiles. Notably, Chlamydia was strongly associated with disease severity, while several other taxa were linked to inflammatory biomarkers and SCFA concentrations. Collectively, these findings support a holobiont-driven model of BRDC in which disease severity emerges from interactions among pathogens, host inflammatory responses, and microbiota-associated functions. The stronger associations observed in the intestinal microbiota, along with links between gut bacteria, SCFAs, and disease outcomes, provide evidence for a functional gut-lung axis in calves and highlight microbial metabolism as a potential target for strategies to improve respiratory health and reduce antibiotic use.

microbiology↗

bioRxiv2026

Mucosal architecture, microbiota resilience and metabolic disruption reveal holobiont dynamics during bovine respiratory disease

The gut-airway axis is increasingly recognised as an important determinant of respiratory health in livestock. However, the interactions among respiratory infections, microbial communities, mucosal barrier function, and microbial metabolism that underpin this axis remain poorly understood. Here, we combined longitudinal immunological, mucosal, microbiological, and metabolic analyses to characterise host-microbiota interactions during antibiotic treatment and experimental bovine respiratory disease (BRD). We found that the bovine respiratory tract is organised as a hierarchically structured mucosal ecosystem, with compartment-specific mucin expression patterns associated with distinct microbial communities. Within this framework, increasing respiratory pathogen loads were associated with greater clinical severity, oxidative stress, acute inflammation, and targeted alterations in mucosal regulation and microbial composition, while serum amyloid A emerged as the host biomarker most closely reflecting infection intensity. Although infection altered host and microbial states, antimicrobial treatment represented the dominant ecological perturbation. Antibiotic exposure reshaped both respiratory and intestinal microbial communities, reducing diversity, increasing community drift, and driving coordinated ecological transitions across the gut-airway axis that exceeded the effects of infection alone. Importantly, these compositional changes were accompanied by profound reductions in acetate, propionate, butyrate, and valerate, identifying short-chain fatty acids as a major functional consequence of gut microbiota disruption. Integrative multi-omics analyses revealed that mucosal organisation, microbial diversity, microbial metabolism, and immune activity were embedded within a highly structured gut-airway network. Together, these findings support a holobiont view of BRD in which disease outcomes emerge not only from pathogen-host interactions but also from ecological disturbances that propagate across interconnected mucosal compartments. Notably, antimicrobial treatment affected ecosystem structure and function more than infection itself, highlighting potential trade-offs between pathogen control and microbiota stability. Preserving microbial resilience and its metabolic functions may therefore represent an important component of future strategies to improve respiratory health and disease resilience in cattle.

systems biology↗