Tissue-Specific Bioactive Metabolites and Antioxidant Activity in Minicitrus (Fortunella hindsii) and Responses to a Fruit-Associated Weissella Strain

Minicitrus (Fortunella hindsii) is a wild kumquat with potential nutritional and medicinal value, but its tissue-specific bioactive metabolites, antioxidant activity, and endophytes remain poorly characterized. Here, we integrated LC-MS profiling, HPLC quantification, chemical and cellular antioxidant assays, 16S rRNA gene sequencing, bacterial isolation, and treatment experiments across five tissues. Among all the metabolites determined by HPLC, 13 were quantified using authentic standards and 24 were semi-quantified as linarin equivalents. Leaves, stems, and fruits accumulated abundant flavone glycosides, with phloretin-3′,5′-di-C-glucoside reaching 1823.19 ± 278.71 μg/g FW in leaves and 847.11 ± 27.28 μg/g FW in fruits, while roots and seeds showed distinct coumarin- and furanocoumarin-rich profiles, respectively. Leaf extracts showed the strongest chemical and cellular antioxidant activities, followed by fruit extracts. Isoorientin 2″-O-rhamnoside and diosmin exhibited strong chemical antioxidant capacity, and several flavone glycosides showed protective effects in cellular assays. Endophytic bacterial communities differed markedly among tissues, with fruit harboring a distinct community dominated by Weissella and Pantoea, which accounted for 65.64% and 19.13% of the relative abundance, respectively. Among two culturable fruit-associated isolates, Weissella sp. SJG-1 treatment was associated with 32.92–104.45% increases in six HPLC-quantified metabolites and higher antioxidant activity of fruit extracts. These findings highlight minicitrus as a source of bioactive metabolites and suggest a potential association between fruit-associated bacteria and fruit functional properties.