Oral microbiome is essential for maintenance of oral cavity health. Imbalanced oral microbiome causes periodontal and other diseases. It is unknown whether oral microbiome affect oral stem cells function. In this study, we used a common clinical anti-biotic treatment approach to alter oral microbiome ecology and examine whether oral mesenchymal stem cells (MSCs) are affected. We found that altered oral microbiome resulted gingival MSCs deficiency, leading to a delayed wound healing in male mice. Mechanistically, oral microbiome release LPS that stimulates the expression of microRNA-21 (miR-21) and then impair the normal function of gingival MSCs and wound healing process through miR-21/Sp1/TERT pathway. This is the first study indicate that interplay between oral microbiome and MSCs homeostasis in male mice.