In vitro assessment of the impact of astragalus, pineapple stem and bergamot extracts on human fecal bacteria

Background: Botanical extracts are increasingly incorporated into functional foods and dietary supplements due to their purported health benefits; however, their impact on the healthy adult gut microbiota remains insufficiently characterized. This study aimed to assess the microbiota-modulating potential of three commercially relevant botanicals (Astragalus membranaceus root extract, pineapple stem extract, and bergamot extract) in both native and digested forms, simulating gastrointestinal passage via the standardized INFOGEST protocol. Methods: Antimicrobial activity was first evaluated in monocultures of nine gut-associated bacterial strains representative of the healthy adult intestinal microbiota, including Lactobacillus acidophilus LA14, Lacticaseibacillus paracasei DG, Hafnia alvei HA4597, Bifidobacterium longum BB536, and B. animalis subsp. lactis BL-04. Botanicals were tested up to a supraphysiological concentration (100 mg/mL, worst-case exposure). Subsequently, each extract (native and digested) was incubated for 48 h under anaerobic conditions with a complex bacterial consortium derived from multiple fecal aliquots obtained from a single healthy adult donor. Microbial composition was assessed using 16 S rRNA gene profiling. α-diversity (Shannon index) and β-diversity (Bray-Curtis distances) were computed, and differential abundance was analyzed. Results: In monoculture, botanical extracts exhibited minimal and strain-specific antimicrobial activity at 100 mg/mL, with inhibition observed primarily for Akkermansia muciniphila, Bacteroides fragilis, and Collinsella aerofaciens. In the fecal consortium model, none of the botanical treatments, regardless of digestion status, produced significant alterations in α- or β-diversity. Modest taxonomic changes were detected, including a reproducible decrease in Collinsella spp. following treatment with digested Astragalus extract. Notably, core beneficial taxa such as Faecalibacterium prausnitzii and A. muciniphila remained unaffected. Conclusions: At physiologically relevant concentrations, Astragalus membranaceus, pineapple stem, and bergamot extracts, in both native and digested forms, do not induce disruptive effects on the structure of the human gut microbial community, supporting their microbiome compatibility under the conditions tested.