Metagenomic Applications in the Diagnosis of Reproductive Disorders in Ruminants: Subject Review

This study demonstrates that the application of metagenomics to the investigation of reproductive disorders in cattle, sheep and goats improves the sensitivity of pathogen detection by approximately 40 % compared with traditional culture and single-target PCR methods. In addition, metagenomic profiling uncovers disorder-specific microbial signatures: Bacteroides–Fusobacterium–Trueperella predominate in postpartum metritis/endometritis, and Enterococcus/Mycoplasma in repeat-breeder syndrome, while high Prevotella load is associated with sperm DNA fragmentation and male subfertility. A working diagnostic cut-off for pathological dysbiosis, =/> 10 % dominance of a specific pathogenic genus combined with a Shannon diversity index < 2, was suggested. The standardized workflow recommended here (i.e., immediate −80 °C sample freezing, DNA extraction, library prep, and sequencing) can result in a clinically actionable report in 24 h and a per-sample cost ≈ US $25 with batch processing. Remaining challenges include laboratory/reagent contamination risk, equivocal ruminant-specific reference databases, international interpretive standards for reporting, and greater cost compared to multiplex qPCR methods. However, handheld Nanopore devices for on-field analysis within < 30 min, integration of metagenomics with transcriptomics, high-resolution machine-learning models, region-specific microbiome atlases, and microbe-targeted interventions (probiotics, phage therapy) collectively signal a shift from reactive to preventive and predictive fertility management—supporting sustainable meat and milk production by lowering dependence on broad-spectrum antibiotics.