Integrating Host Transcriptomics and Metagenomics in the Periparturient Dairy Cow: From Molecular Signatures to Host–Microbiome Interfaces

The periparturient or transition period—roughly three weeks before to three weeks after calving—compresses the most severe metabolic, endocrine and immunological demands of the production cycle into a few weeks and accounts for most clinical disease and involuntary culling in dairy herds. Conventional surveillance relies on downstream indicators—non-esterified fatty acids, β-hydroxybutyrate, calcium and acute-phase proteins—that document failed adaptation without resolving its regulatory origins. Two omics platforms now close that gap. Transcriptomics shows that the liver, adipose tissue, mammary gland, endometrium, rumen epithelium and circulating leukocytes each execute a distinct, temporally ordered program organized around lipid mobilization, gluconeogenesis, endoplasmic reticulum stress, redox defense and inflammatory resolution, layered over a regulatory tier of non-coding RNAs. Metagenomics shows in parallel that rumen, hindgut, uterine, vaginal, teat-apex and colostrum communities are restructured by parturition and by the dietary shift into lactation, with reproducible dysbiotic signatures accompanying ketosis, fatty liver, metritis, endometritis and intramammary infection. Critically, the two layers are mechanistically coupled: microbial short-chain fatty acids, secondary bile acids, purine derivatives and amino acids reprogram hepatic and immune cell transcription, while host lipolysis, inflammation and mineral demand reshape community structure. This review synthesizes both groups of literature within a single framework, formalizes five host–microbiome interfaces supported by paired measurements and identifies the biomarker, nutritional and genetic-selection opportunities that emerge only when host and microbial evidence are read together.