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

The successful establishment of the bacterial community in the gastrointestinal tract (GIT) 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 in respect to the different genetic backgrounds and the type of -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 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 demonstrating the robustness of the analysis. Breed-specific differences were noted at the genus level, and minor effects of milk type (based on ß-casein content) were detected. A significant interaction was detected between calf age and bacterial abundance, but only partially for milk or breed. The method for analysing and evaluating saliva samples provided valuable insights into the development of the microbiota in the oral cavity and the forestomachs under the influence of breed and the milk fed by the successful separation of oral- and rumen- associated bacteria. Based exclusively on samples taken from the oral cavity, invasive examination methods could be avoided to a greater extent in the future and only serve as supporting points for analyses.