Microbiota is now considered as a major determinant of holobiont phenotypes. The present study aimed at exploring microbiota associated to various body sites of dairy cows to 1) identify determinants of the microbiota composition and 2) evaluate the intra- and inter-animal microbial sharing. Microbiotas from the mouth, nose, vagina and milk of 45 primiparous lactating dairy cows were characterized 1 week pre-partum and 1, 3, and 7 months post-partum by metataxonomics. Cows with different scores of susceptibility to mastitis were used, as defined by the French national genomic evaluation system (genotyping). Data were analysed using the DADA2 pipeline. Statistical analyses on a- and b-diversity were performed using R and specialized packages (phyloseq, DESeq2). Microbiota differed between body sites and changed over the lactation as a result of physiological and environmental changes (from indoor with corn and grass silage to outdoor). An important sharing of microbes was revealed within animals between nearby anatomic sites (up to 32% of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota) but also between distant ones (e.g. milk with nasal microbiota). In contrast, microbes shared between animals within the herd were limited (<7% of ASVs shared by more than 50% of the herd for a given site and time point) and they were mainly found in the mouth and nose. Although they shared a common environment and diet, each animal thus hosted a specific set of bacteria, suggesting a host control. Interestingly, the score of susceptibility to mastitis was slightly related to the milk microbiota composition, confirming a link between host genetics and microbiota. In conclusion, this work highlights an important intra-animal sharing of microbes between different body sites, whereas sharing of microbes was limited between animals within the herd, supporting a host regulation of body-associated microbiotas. A better understanding of the host determinants shaping microbiota will allow to modulate the host-microbiota interplay for health and production.