Distinct gut viral communities across life stages in dairy cattle

Abstract Background Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages shape microbial communities in many ecosystems, their role across dairy cattle life stages is unknown. We characterized DNA viral community composition, diversity, and ecology in cows belonging to four life stages: calf, heifer, dry adult, and lactating adult. Results Using hybrid Illumina and Oxford Nanopore sequencing, we assembled 30,321 viral operational taxonomic units from fecal samples, including 1338 complete genomes (92% representing novel genera). Viral communities showed distinct life-stage stratification. Calves harbored low-diversity communities (Shannon index: 2.49 vs >6.58 in adults). They also showed a higher proportion of temperate phages (49% vs <24% in adults), though this difference was not statistically significant given the small calf sample ( n = 3). Adult viromes showed 50-fold higher community evenness than calves. Viral and bacterial diversity were inversely correlated (Spearman’s rho = −0.69), with viral diversity peaking during the drying-off period when bacterial diversity was lowest. Dry cows showed the highest viral loads (3.61% of microbial DNA vs 1.52% in lactating cows) and elevated virus-host ratios, coinciding with increased positive selection on viral genes. Twenty-six vOTUs targeting the methanogen Methanobrevibacter were detected in adults but not calves, paralleling a 757-fold higher relative abundance of Methanobrevibacter in adults. Additionally, we identified viruses carrying putative auxiliary metabolic genes involved in methane metabolism pathways. Conclusions The dairy cattle gut virome is extensive, almost entirely novel, and clearly stratified by life stage—characterised here across calves, heifers, dry adults, and lactating adults for the first time. Viral and bacterial diversity showed a significant inverse relationship that was most pronounced around drying-off, and viruses targeting the methanogen Methanobrevibacter were present in adults but absent from calves. Although cross-sectional, the data establish life stage as a key variable in the ruminant gut virome and identify methanogen-infecting phages as a candidate for reducing enteric methane emissions.