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The need for safer therapeutics contra gastrointestinal infections with lowered harmful effect on positive gut microbiota is discussed in this work, mainly in respect to the increasing pathogen resistance to antibiotics. Since many phytocompounds possess strong specific antimicrobial activity, this work is focused on selectively acting plant-derived products in the context of their inhibitory activity towards gut pathogens versus their reduced impact on beneficial resident gut microbiota of humans. Resulting from the experimental part, a natural alkaloid 8-hydroxyquinoline (8HQ) was selected as the phytocompound with the most pronounced selectivity out of the 26 plant-derived products tested. Its activity was scrutinized also by a method combining fluorescent in situ hybridization and flow cytometry. Furthermore, the selectivity of 8HQ was practically utilized for development of improved selective medium for bifidobacteria isolation from feces. Conclusively, further research of phytocompounds as safer antibacterial agents is suggested.