Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity

Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.