Microbiome最新文献

{"title":"Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.","authors":"Chunlong Wang, Shitong Li, Yiwo Liu, Xinyue Zhao, Fusen Wang, Yimin You, Xiyang Zhao","doi":"10.1186/s40168-026-02453-2","DOIUrl":"10.1186/s40168-026-02453-2","url":null,"abstract":"<p><strong>Background: </strong>Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct​ functional potential, thereby improving tree nutrition.</p><p><strong>Results: </strong>Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.</p><p><strong>Conclusions: </strong>Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148317878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.","authors":"Katie Lawther, Nicholas J Dimonaco, Paul Donnelly, Abdulai Guinguina, Sophie J Krizsan, Sharon A Huws","doi":"10.1186/s40168-026-02447-0","DOIUrl":"10.1186/s40168-026-02447-0","url":null,"abstract":"<p><strong>Background: </strong>Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH₄) accounting for 33% of anthropogenic emissions. CH₄ is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH₄ emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.</p><p><strong>Results: </strong>ASP supplementation reduced CH₄ yield by 54% (g CH₄/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH₄ were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION : ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13295230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148239726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Maternal intestinal L. vaginalis facilitates embryo implantation and survival through enhancing uterine receptivity in sows.","authors":"Qianhong Ye, Yifan Hu, Haoyi Jiang, Tingting Luo, Longshan Han, Yuwen Chen, Jiaying Chen, Libao Ma, Ziyi He, Xianghua Yan","doi":"10.1186/s40168-026-02459-w","DOIUrl":"10.1186/s40168-026-02459-w","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13263924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148239744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dismissing-then-recruiting: a unique mechanism for symbiont recruitment and lignocellulose degradation in gut of black soldier fly larvae.","authors":"Fang Ming Xiang, Xiao Tian Tang, María Gómez Brandón, Ahmed R Henawy, ShuoYun Jiang, XinHua Xu, XueXin Chen, ZhiJian Zhang","doi":"10.1186/s40168-026-02441-6","DOIUrl":"10.1186/s40168-026-02441-6","url":null,"abstract":"<p><strong>Background: </strong>Black soldier fly larvae (Hermetia illucens L., BSFL) efficiently degrade lignocellulosic waste despite lacking endogenous lignocellulolytic enzymes, indicating a critical dependence on gut-associated microbiota. However, how BSFL are associated with the enrichment and spatial organization of lignocellulose-degrading symbionts within the gut remains poorly understood.</p><p><strong>Results: </strong>We show that BSFL establish a spatially structured microbiome through gut compartment-specific immune regulation. Axenic larvae showed negligible lignocellulose degradation, whereas microbiota-associated larvae achieved ~ 33.3%, confirming microbial dependence. Antimicrobial peptides, including cecropin and defensin, were highly expressed in the anterior midgut, forming a selective barrier. In contrast, the posterior midgut showed reduced immune activity via peptidoglycan recognition proteins (PGRP-LB, PGRP-SC). Concurrently, host glycosylation-related genes (C1galt1, GlcAT-P, FUT8/11) were significantly upregulated in the posterior midgut (17-19 TPM), representing a 4-fivefold increase relative to the anterior region (p < 0.01). This region was correspondingly enriched in carbohydrate-active symbionts producing glycoside hydrolases, including galactosidases, fucosidases, and mannosidases, suggesting that upregulated glycan biosynthesis may provide sustained nutrient availability for microbial taxa with corresponding carbohydrate-utilizing capacities. Such compartmentalized immune-metabolic coordination is consistent with a potentially conserved strategy for modulating immune tolerance and fostering symbiont recruitment.</p><p><strong>Conclusions: </strong>Collectively, our findings define a compartmentalized \"Dismissing-then-Recruiting\" strategy for microbiome assembly in BSFL, which is associated with the structuring of functional symbiont communities for efficient lignocellulose bioconversion, thereby elucidating novel principles for sustainable waste management. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148211946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.","authors":"Alizée Le Moigne, Adrian-Ştefan Andrei, Jakob Pernthaler","doi":"10.1186/s40168-026-02442-5","DOIUrl":"10.1186/s40168-026-02442-5","url":null,"abstract":"<p><strong>Background: </strong>Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-\"functional dispersal limitation\"-explained variation in cellobiose use.</p><p><strong>Results: </strong>Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of \"functional dispersal limitation.\" We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.</p><p><strong>Conclusions: </strong>Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148204822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.","authors":"Chao Wei, Yaxiang Wang, Zhe Chen","doi":"10.1186/s40168-026-02445-2","DOIUrl":"10.1186/s40168-026-02445-2","url":null,"abstract":"<p><strong>Background: </strong>The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood.</p><p><strong>Results: </strong>Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188 kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems.</p><p><strong>Conclusions: </strong>Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13465236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148199412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.","authors":"J Krull, C Sidhu, V Solanki, M Bligh, L Rößler, R K Singh, G Huang, C S Robb, H Teeling, P H Seeberger, T Schweder, C J Crawford, J-H Hehemann","doi":"10.1186/s40168-026-02451-4","DOIUrl":"10.1186/s40168-026-02451-4","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13242660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148194915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.","authors":"Selina Stahl, Hanna Widmaier, Vadim Sakk, Kodandaramireddy Nalapareddy, Ann-Kathrin Kissmann, Frank Rosenau, Medhanie A Mulaw, David B Haslam, Hartmut Geiger","doi":"10.1186/s40168-026-02428-3","DOIUrl":"10.1186/s40168-026-02428-3","url":null,"abstract":"<p><strong>Background: </strong>Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.</p><p><strong>Results: </strong>Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4⁺ and CD8⁺ T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1^-/- recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.</p><p><strong>Conclusion: </strong>Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13242121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148176170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.","authors":"Danni Guo, Yuanyuan Chen, Yahong Wu, Jingmin Cheng, Yawen Lin, Wenjie Lai, Wentao Ma, Hang Yang, Lianyi Han, Lan Ma, Haidong Jia, Xiao Liu","doi":"10.1186/s40168-026-02433-6","DOIUrl":"10.1186/s40168-026-02433-6","url":null,"abstract":"<p><strong>Background: </strong>Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.</p><p><strong>Results: </strong>To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.</p><p><strong>Conclusions: </strong>Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148157250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host-guided microbiome-metabolite interactions enable cross-kingdom SynComs for disease suppression.","authors":"Shanshan Liu, Shuxian Wang, Jingyuan Zhang, Chengyuan Tao, Mohammadhossein Ravanbakhsh, Xu Xu, Kaiqi Wen, Dandan Xiang, Ou Sheng, Zongzhuan Shen, Chunyu Li, Rong Li, Qirong Shen, George A Kowalchuk","doi":"10.1186/s40168-026-02430-9","DOIUrl":"10.1186/s40168-026-02430-9","url":null,"abstract":"<p><strong>Background: </strong>The plant microbiome plays a crucial role in enhancing disease resistance, yet microbiome-based plant protection strategies remain limited by an incomplete understanding of how host selection, microbial interactions, and rhizosphere chemistry jointly shape pathogen suppression.</p><p><strong>Results: </strong>Here, we adopt a \"learning from nature\" approach to design synthetic microbial communities (SynComs) that recapitulate naturally evolved disease-suppressive interactions, using banana Fusarium wilt as a model system. High-throughput profiling revealed that both bacterial and fungal communities contribute to varietal resistance. Resistance-associated microbial taxa were identified and isolated to assemble bacterial, fungal, and cross-kingdom SynComs representative of resistant versus susceptible hosts. SynComs derived from resistant varieties suppressed pathogen growth more effectively than those from susceptible hosts, with cross-kingdom SynComs exhibiting the strongest effects. Cross-kingdom SynCom inoculation significantly reduced disease severity and restructured both the composition and functional potential of the rhizosphere microbiome. Integrative transcriptomic and metabolomic analyses revealed coordinated host metabolic reprogramming, characterized by increased accumulation of diverse metabolites, including alkaloids, amino acids, and flavonoids. Notably, supplementation with resistance-associated rhizosphere metabolites, such as stearic acid and shikimic acid, further enhanced disease suppression.</p><p><strong>Conclusions: </strong>Together, our findings establish a mechanistic framework in which host-guided microbiome assembly and metabolite-mediated interactions jointly enable effective cross-kingdom SynComs for disease suppression, providing ecological principles for microbiome-based plant protection strategies. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148157258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}