Background Immunoglobulins target both pathogens and commensal microorganisms, yet the purpose of this recognition remains unclear. We hypothesised that immunoglobulin-associated microbial communities, particularly bacteriophage, contribute to early-life microbiome establishment and immune development. Methodology Bovine colostrum and chicken egg yolk were analysed as models of maternal immune transfer. Shotgun metagenomics and 16S rRNA sequencing were used to characterise immunoglobulin-associated bacterial, viral and fungal communities. IgG-, IgA- and IgY-bound fractions were examined, and microscopy was used to confirm immunoglobulin-microbe associations. Results In cattle, colostrum bacteriophage communities were highly animal-specific despite shared housing and feeding conditions, with lactococcal phages predominating before first feeding. Scanning electron microscopy confirmed the presence of IgA-associated bacteriophage. Minimal overlap between maternal faecal and colostrum bacterial communities suggested that faecal microbiota contribute little to initial neonatal colonisation. In chickens, yolk-derived IgY recognised a diverse immune biome comprising bacteria, bacteriophage and fungi. Strong flock-specific differences were observed, with a commercial Hyline flock displaying markedly reduced microbial diversity compared with a backyard French Copper Black Marans flock. Viral diversity reflected bacterial community structure, while fungal communities were largely absent in the less diverse flock. Microscopy confirmed IgY-associated microorganisms. Discussion These findings demonstrate that immunoglobulins selectively recognise complex microbial communities across mammalian and avian species. The transfer of an immunoglobulin-associated immune biome through colostrum and egg yolk may represent an evolutionarily conserved mechanism that supports microbiome establishment, immune tolerance and the orderly development of the neonatal immune system.