Pathogenic bacteria is a major health problem that causing a large number of diseases and their treatments with antibiotics lead to the appearance of bacterial resistance to antibiotics. Moreovere, the use antibiotics eliminated the beneficial bacteria from the gastrointestinal tract, thus the effect of some plant extract. Three plants, Pimpinella anisum, Syzygium aromaticum and Punica granatum, used traditionally as medicine or food additive, were extracted and their inhibitory effects on four pathogenic bacteria and two genera of gut microbiota were determined. It was shown that all tested plant extracts showed an inhibitory effect on pathogenic bacteria, while gut microbiota was affected only by S. aromaticum and P. granatum extracts. The MIC of the methanolic extracts of the used plant extracts ranged from 3.1 to 93.7 mg/ml and no toxicity was found on Artemia salina of Pimpinella anisum. Additionally, P. anisum was increased the cell count of Bifidobacterium by studying the growth curve of gut microbiota.