(1) Background: The aim of the study was to compare the potency of Plantago media L. (Plantaginaceae) extracts on Acanthamoeba sp. trophozoites, which are opportunistic protozoan parasites leading to several dangerous diseases; (2) Methods: The chromatographically (TLC, HPLC-DAD) characterized water fractions of the extracts from biomass from in vitro cultures (shoots and roots), leaves, and inflorescences from field cultivation were used for the study of the acanthamoebic activity in a Thoma haemocytometer chamber; (3) Results: The anti-amoebic effect at the lowest concentration (1.0 mg/mL) was demonstrated only by the extract of the leaves from the cultivation (50.50% inhibition). The remaining samples inhibited the growth of parasites from a concentration of 5.0 mg/mL in the range of 41.36% inflorescences to 63.89% shoots in vitro. Quantitative determinations of phenolic compounds in the tested extracts indicate a tendency to increase the potency of the anti-amoebic effect with the content of a phenylethanoid glycoside—acteoside. The maximum content of this compound was determined in leaves from field cultivation (6.64%) and the minimum in inflorescences (0.65%). This is confirmed by the range of the lowest IC50 values (the strongest biological activity) for the tested samples, 0.95–1.80 mg/mL for leaves from cultivation, and the high values, 9.70–5.30 mg/mL for inflorescences and in-vitro-derived roots. The strength of the biological activity of the extracts correlated with the content of acteoside, which constituted 84–93% of the sum of phenolic compounds determined; (4) Conclusions: The performed investigations proved the anti-acanthamoebic efficacy of Plantago media organs, including those obtainable by biotechnological methods, and indicated phenylethanoid glycosides, their main phenolic constituents, to be responsible for the activity. To our knowledge, this is the first report on the amoebicidal activity of Plantago media extracts from biomass produced by biotechnological methods and organs of an intact plant.
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