The human gut microbiota is a large and diverse microbial community that inhabits the gastrointestinal tract and provide multiple benefits for us including nutrient absorption, maturation of the immune system, and also plays a central role in protection of the host from pathogenic bacterial infection [1]. On the other hand, many enteric pathogens have developed strategies in order to be able to outcompete the gut community, leading to infection and/or chronic diseases [2]. Phylogenetic analysis can be effective in choosing the appropriate antibiotics that have the greatest effect on pathogenic bacteria and least impact on the normal human gut flora. The 16S rRNA gene sequences for 50 species of human gut microbiota and pathogenic bacteria were downloaded from GenBank and aligned using Clustal Omega. The tree was constructed using the Maximum-likelihood method in MEGA-X [3]. Also, bacterial diversity in environmental samples was analyzed using RDP Classifier v.2.12 [4]. The Species of Collinsella aerofaciens, the most abundant actinobacterium in the gastrointestinal tract of healthy humans, are closely related to other normal gut bacterium Bifidobacterium animalis. Clostridium, includes several significant human pathogens, are closest strains to genus of Clostridioides which includes Clostridioides difficile, a human pathogen causing an infectious diarrhea. Bacillus cereus cause infections of the gastrointestinal tract and surprisingly, the closest strains to this pathogen are Streptococcus salivarius and Streptococcus viridans which are normal human oral bacteria. Vibrio cholerae share close relationship with the other causal agents of the infections of the gastrointestinal tract, Yersinia, Escherichia coli, Shigella and Salmonella. Campylobacter jejuni closely related to Helicobacter pylori. Based on the phylogenetic analysis there are close relationship between human gut microbiota but only some of them are related to gut pathogenic bacteria. In general, this phyl
