Core microbial populations drive longitudinal development of the hindgut bacterial microbiota in Jersey calve

ABSTRACT The early-life gut microbiome represents a critical window during which microbial succession may exert lasting effects on host metabolism and productivity. While gut microbiome–host phenotypic associations have been extensively studied in Holstein calves, such relationships are rarely reported in alternative breeds, including Jersey calves. We hypothesized that Jersey calves would exhibit age-dependent community shifts characterized by core microbial populations and breed-associated bacterial networks that may contribute to metabolic phenotype. Fecal samples were collected from dams post-calving, and Jersey calves ( n = 12) were sampled longitudinally at 24–48 h and weekly through 12 weeks. Bacterial communities were profiled using the V1–V2 region of the 16S rRNA gene. The number of observed ASVs and Shannon diversity increased with age ( P < 0.001), and Beta diversity revealed age-dependent structuring (weighted R ² =0.12, P = 0.023; unweighted R ² =0.37, P = 0.001), with calf communities gradually converging toward dams. Taxonomic analyses revealed a conserved core microbiome comprising 34 taxa accounting for over 90% of total community abundance. Neonatal samples were dominated by facultative anaerobes, including Escherichia and Streptococcus , with early colonization by Blautia and Collinsella . Calves then exhibited transient enrichment of milk-glycan-associated taxa, including Lactobacillus and Bacteroides . Weeks 3–7 stages saw preeminence of acetogens ( Blautia , Dorea, Collinsella ), followed by later enrichment of adult-associated fiber-degrading taxa. Collectively, these findings demonstrate a consistent age-dependent pattern of hindgut microbiome maturation among Jersey calves. The taxonomic patterns provide a foundation for investigating potential links between early-life microbial ecology and breed-specific metabolic phenotypes. IMPORTANCE The neonatal period represents a critical window for microbial community assembly and interaction with the host. While microbial succession in Holstein calves has been studied extensively, little is known about microbiome assembly in Jersey calves. Herein, we performed longitudinal profiling of the hindgut microbiome of Jersey calves from birth through twelve weeks of age. Microbial communities underwent a structured succession broadly resembling patterns reported previously in Holsteins, with network analyses revealing microbial assemblages that shift with diet throughout the pre- and postweaning periods. Jersey calves also exhibited a notably elevated abundance of several acetate-associated taxa during early life. These findings provide the first detailed characterization of hindgut microbiome assembly in Jersey calves and identify microbial community structures potentially linked to breed-specific metabolic phenotypes. Such information is critical for designing microbiome-targeted strategies to improve calf growth, health, and feed efficiency, and for influencing milk components.