Fig. 1

Experimental design and associated metadata. A Microbiota associated to four different anatomic sites, namely oral, nasal and vaginal cavities as well as the internal teat cavity/foremilk (hereafter referred as to milk) was characterized on 45 primiparous cows at four different time points, 1 week before parturition (-1W, except for milk) and 1, 3 and 7 months post-partum (1 M, 3 M, 7 M). The relationship between microbiota and host genetics was considered by using cows with different scores of susceptibility to mastitis (SM score). These cows arose from two divergent lines of cows resistant or susceptible to mastitis [21]. An additional score was included, corresponding to the body condition (BC). B Diet (rations R1, R2, R3 or G—grazing) and housing conditions (purple: indoor housing 1, blue: indoor housing 2, orange: indoor housing 3, green: grazing) for the 3 groups of animals (see Additional file 1 for details on housing and diet). *Grazing combined with corn silage