Integrated metabolomics and microbiome analyses reveal nutritional differences between yellow and white maize (Zea mays L.) kernels

Yellow maize kernels accumulated up to 5.45 μg/g lutein and 15.30 μg/g zeaxanthin. • White maize contained only trace carotenoids but distinct phenolic-rich profiles. • Fusarium and Aspergillus were fungal biomarkers of yellow and white maize. • 313 differential metabolites were linked to carotenoid and phenylpropanoid pathways. Maize ( Zea mays L.) is a globally significant cereal crop that exhibits wide phenotypic and nutritional diversity. Yellow maize is highly valued for its accumulation of health-promoting carotenoids, whereas the functional profile of white maize is characterized by distinct classes of secondary metabolites. However, the complex interplay among host genetics, the kernel endophytic microbiome, and the associated metabolic profiles remains poorly understood. In this study, we employed an integrated approach combining targeted carotenoid quantification, 16S rRNA and ITS amplicon sequencing, and untargeted metabolomics to comparatively analyze the internal microenvironments of yellow and white maize kernels. Phenotypic analysis confirmed that yellow maize kernels accumulated substantially higher concentrations of lutein (up to 5.45 μg/g) and zeaxanthin (up to 15.30 μg/g) relative to the trace amounts detected in white maize. Microbiome profiling revealed that host genotype profoundly shaped endophytic community assembly: although bacterial alpha diversity was comparable between the two groups, yellow maize harbored significantly higher fungal alpha diversity. Taxonomic analysis identified distinct microbial biomarkers, with Fusarium being identified as a fungal biomarker enriched in yellow maize, whereas Aspergillus was enriched in white maize and Pseudomonas dominated its bacterial community. Furthermore, untargeted metabolomics identified 313 differentially accumulated metabolites, predominantly comprising lipids, organic acids, and phenylpropanoids. KEGG enrichment analysis demonstrated that pathways related to phenylalanine, tyrosine, and tryptophan biosynthesis, plant hormone signal transduction, and ABC transporters were significantly enriched, indicating divergent metabolic profiles between the two cultivar groups. Collectively, these findings reveal consistent associations between host secondary metabolism and selectively enriched endophytic microbiomes, providing novel metabolic and microbial targets for future precision breeding and nutritional biofortification in maize.