ArticleMicrobiome2025
Host metabolites explain microbiome variation between different rice genotypes.
Article in Microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco.Plant physiology · 2026Article
- From genotype to microbiome function: a gene-metabolite-microbiome pathway shaping plant nutrient acquisition.The New phytologist · 2026Article
- Review
- Functional Portability of a Hyperaccumulator-Derived Core Microbiome: Enhancing Cadmium Phytoextraction inToxics · 2026Article
- Chemical whispers hidden in the plant and microbiota kingdoms.Nature reviews. Microbiology · 2026Article
- Cover cropping enhances fruit quality in protected citrus cultivation by modulating rhizosphere microbiome and iron availability.Frontiers in plant science · 2026Article
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Authors and funding
13 authors.
Funding
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Abstract
backgroundPlants live in close association with microbial communities that support their health and growth. Previous research has indicated that the composition of these communities can differ between genotypes of the same plant species. Host-related factors causing this variation are mostly unknown. Microbiome genes, or M genes in short, are host genes that are involved in shaping the microbiome. We hypothesized that specific M genes are responsible for microbiome variation between rice genotypes and that it is connected to plant metabolites controlled by these genes.
resultsOur study was aimed at identifying plant metabolites driving genotype-specific microbiome assembly and establishing a link to host genetics. Targeted metabolite quantification was combined with microbiome profiling of the rice phyllosphere microbiome, association analyses on single-nucleotide polymorphism (SNP) level, and genetic modifications to validate microbiome-shaping effects of the discovered M genes. Targeted metabolite quantifications revealed that phenylpropanoid concentrations in rice leaves can substantially differ among 110 representative genotypes grown under the same, controlled conditions. Redundancy analyses (RDA) showed that these metabolites can explain 35.6% of the variance in their microbiomes. Further verification experiments resulted in the identification of two M genes. OsC4H2 and OsPAL06 are both plant genes with microbiome-shaping effects, mainly via their role in ferulic acid biosynthesis. Targeted gene mutation experiments confirm that distinct phyllosphere-associated bacterial groups are highly responsive to the discovered M genes.
conclusionThis study provides detailed insights into the links between host genetics and microbiome variation in plants. Knowledge about host genes that are in control of the microbiome paves the way for microbiome engineering and targeted plant breeding approaches. Video Abstract.
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