Effect of β-casein A1 or A2 milk on microbiota composition in Holstein, Simmental and crossbred dairy calves of both sexes

Abstract The successful establishment of the bacterial community in the gastrointestinal tract is of crucial importance for growth, metabolic health, performance and welfare in early and later stages of ruminants. This study aimed to investigate the development of oral- and rumen-associated bacteria in pre-weaning calves and to compare them with respect to the different genetic backgrounds and the type of $\beta $ -casein in the milk fed. Calves were kept in the same defined nutritional and housing environment. Saliva samples were taken at three time points up to 27 days of age before weaning via buccal swabs, and the extracted DNA was analysed using 16S rRNA gene amplicon sequencing. The development of the microbiota in the rumen and oral cavity was differentially analysed and evaluated. Age-dependent changes were observed, with a clear shift in rumen-associated bacteria over time and increasing alpha diversity, while oral-associated bacteria stabilized more rapidly at a young age, demonstrating the robustness of the analysis. Breed-specific differences were noted at the genus level, and minor effects of milk type (based on β-casein type) were detected. A significant interaction was detected between calf age and bacterial abundance, as well as between the breed and bacterial abundance, but not for milk type. The method for analysing and evaluating saliva samples provided valuable insights into the development of the microbiota in the oral cavity and the rumen under the influence of breed and the milk fed by the successful separation of oral- and rumen-associated bacteria. Due to the exclusive use of samples from the oral cavity, invasive examination methods could be largely avoided in the future and would only serve as additional controls to confirm the results of the buccal swab analyses.