The effect of long-term administration of two different Bacillus strains was tested on 90 breeding sows (Landrace x Yorkshire) that were randomly allotted into three treatments: a control group (CON), supplemented with 5x108 cfu/kg B. subtilis 25841 (PR1), or 5x108 cfu/kg B. amyloliquefaciens 25840 (PR2). Reproductive parameters were registered along three reproductive full cycles. Fecal samples were taken along the third cycle from the sows (on days 8 and 21 of lactation) and from the piglets (on days 21 and 33 (12 post-weaning)). Fecal microbiota was analyzed by sequencing the 16S RNA gene (Illumina MiSeq®) and jejunum samples, obtained from piglets on day 21, analyzed for gene expression (52 genes by OpenArray® plate). Supplemented sows showed higher number of born piglets per litter (P = 0.01) and PR2 sows a higher number of born alive (P = 0.01). Regarding sows’ fecal microbiota, changes were found in community structure (ANOSIM test, P = 0.08) with changes at phylum level (Firmicutes:Bacteroidetes: 3.7, 5.3 and 4.6 for CON, PR1 & PR2, P = 0.10) and at family level (Prevotellaceae: 9.4, 7.3, 7.3% (P = 0.03) and Ruminococcaceae: 16.1, 13.1, 13.7% (P = 0.04)). Several genera were also modified including Prevotella, Ruminococcus and Megasphaera. Regarding the microbiota of piglets, the administration of probiotics to their mothers was associated to structural changes in piglets’ fecal community during lactation (PEnvfit=0.05) but not after weaning, although relevant changes were observed between both periods (PEnvfit< 0.001). The expression of different genes was clearly modified by weaning but we were not able to detect changes related to the probiotic in any of the genes analyzed. In conclusion, the addition of B. subtilis 25841 and B. amyloliquefaciens 25840 were shown to enhance the sow reproductive performance in terms of prolificacy, with a clear impact on the gut microbial ecosystem of the sows and shifts in the microbiota structure of suckling piglets.