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This study was conducted to identify and characterize the Bacillus strain from Goat’s milk in Algeria and to evaluate the prebiotic effect of H. scoparia aqueous extract and ZnO-NPs on the isolated Bacillus strain. Potentially probiotic bacteria were isolated and identified based on phenotypic characteristics, including the morphological, physiological (growth temperature, salt tolerance), biochemical (API 10S strip kits), and confirmed by 16S rDNA gene sequencing. Bacillus pumilus specie of lactic acid bacteria were identified. The base pair length of amplified DNA for the isolate was 1500 Bp. The isolates could not grow at 10°C and 45°C and tolerate up to 6% salt. H. scoparia extract and ZnO-NPs have a beneficial effect on the Bacillus pumilus strain for acid tolerance, bile tolerance, and cell surface hydrophobicity respectively; H. scoparia extract and ZnO-NPs results are high comparing to the control group’s results. As the concentration of the tested samples increases, the percentage of probiotic characteristics of Bacillus pumilus increases, in contrast to the control sample. Therefore, they could be useful tools to define adequate combinations in colonic foods development and health benefits. The beneficial physiological and biochemical properties of isolated Bacillus pumilus space from Goat’s milk with the H. scoparia aqueous extract and ZnO-NPs revealed their potential applications in the food industry.