iMetaPub Date : 2026-08-26Epub Date: 2026-07-13DOI: 10.1002/imt2.70155
Yang Liu, Wanna He, Chunhui Wang, Congyang Yi, Tianxin Guo, Congle Zhu, Qian Liu, Fangpu Han
{"title":"Two near-complete assemblies reveal R-subgenome structural and centromeric divergence associated with reproductive isolation in hexaploid triticale","authors":"Yang Liu, Wanna He, Chunhui Wang, Congyang Yi, Tianxin Guo, Congle Zhu, Qian Liu, Fangpu Han","doi":"10.1002/imt2.70155","DOIUrl":"https://doi.org/10.1002/imt2.70155","url":null,"abstract":"<p>We present two near-complete triticale genome assemblies and perform pan-centromere analyses across >200 haplotypes from parental species, synthetic allopolyploids, cultivars, and 337 resequenced accessions, revealing a shared chromatin framework underlying functional centromeres in all three subgenomes, where wheat- and rye-derived CENH3 co-occupy divergent centromeric repeats. Postpolyploid evolution drives extensive centromere remodeling, including size convergence, repeat turnover, and locus repositioning, with the R subgenome emerging as the primary source of structural and centromeric divergence. In F<sub>1</sub> hybrids, R-subgenome structural and centromeric divergence is associated with meiotic abnormalities, including chromosome misalignment, lagging chromosomes, and micronuclei formation, suggesting a link between centromere variation and reduced meiotic stability.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbiome and aging: Trajectories of microbiome age across human ecosystems and their systemic effects","authors":"Zhexin Ni, Jiaojiao Xie, Zhichun Zhang, Keming Zhang, Jie Ding, Mingyang Chang, Ying Su, Yunan Zhang, Mingfei Yao, Chengyuan Wang, Yan Yan, Wenjie Fang, Hainv Gao, Xuecong Tian, Yangshuo Li, Xinlin Zhu, Wen Zhang, Wanqing Liao, Gaoyuan Xu, Guojing Chen, Xiaoyi Lv, Chaoqin Yu, Weihua Pan, Vadim Molodtsov, Lanjuan Li, Yue Gao, Wei Zhou","doi":"10.1002/imt2.70148","DOIUrl":"https://doi.org/10.1002/imt2.70148","url":null,"abstract":"<p>The “microbiome age,” a computationally derived systemic biosignature, is emerging as a pivotal framework for deciphering host aging trajectories and multi-organ health status. Beyond merely cataloging taxonomic shifts within specific niches, this concept integrates the cumulative biological effects of microbial community structure, functional homeostasis, ecological interactions, and host regulatory dynamics over time. Accumulating evidence indicates that a deviation between chronological and microbiome age-termed the “microbiome age gap”-closely correlates with systemic declines in immunomodulation, metabolic robustness, barrier integrity, and neuroendocrine regulation, positioning it as a potent predictor of healthspan and disease risk. A defining feature of microbial aging is the convergence of divergent ecological niches toward a state of dysbiosis. Despite distinct compositional profiles across the gut, oral cavity, skin, and urogenital tract, these ecosystems commonly exhibit diminished stability, functional remodeling, and altered host–microbe interaction modes with advancing age. Concurrently, site-specific signatures persist, linking microbial shifts to distinct physiological dimensions such as metabolic-inflammatory axes, barrier function, and local hormonal environments. In this review, we systematically delineate the theoretical underpinnings and computational strategies for modeling microbiome age. We synthesize current evidence regarding age-related microbial trajectories across diverse body habitats and propose an integrative framework: microbiome age serves dually as a holistic indicator of systemic aging and a sensitive window into localized organ vulnerability. This perspective not only advances our understanding of host-microbe interactions in aging but also opens new avenues for precision stratification, personalized intervention, and healthspan management.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70148","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche","authors":"Yunhong Shi, Jinpei Lin, Yi Wu, Shengsong Xu, Naiyuan Zhang, Yiji Pan, Anli Ren, Ying Fang, Yu Huang, Xiayin Zhang, Zhuoting Zhu, Yehong Zhuo, Honghua Yu","doi":"10.1002/imt2.70163","DOIUrl":"10.1002/imt2.70163","url":null,"abstract":"<p>Retinal ischemia-reperfusion (RIR) injury is a central mechanism underlying irreversible vision loss in glaucoma and other retinal diseases, yet the spatial organization of the pathogenic microenvironment remains poorly understood. Here, we constructed a high-resolution, whole-eye spatial multi-omics atlas integrating Stereo-seq transcriptomics and MALDI-MSI-based metabolomics to capture the early molecular events in the RIR mouse model. Spatially, retinal ganglion cell (RGC) interactions with surrounding cells were markedly reduced after injury, whereas immune–glial interactions were enhanced, revealing a shift from a neuron-centered to an immunometabolic state. Within the ganglion cell layer (GCL), the primary pathological locus, we identified <i>Trem2</i><sup><i>+</i></sup> microglia that expand in situ, establish close proximity to degenerating RGCs, and exhibit strong spatial association with dysregulated sphingolipid metabolism. Mechanistically, using <i>Trem2</i> knockout mice and microglia-specific <i>Trem2</i> siRNA knockdown, we demonstrate that TREM2 directly binds to SPTLC2, the rate-limiting enzyme of de novo sphingolipid biosynthesis, driving ceramide-centric metabolic reprogramming that modulates the AKT-mTOR signaling axis and amplifies inflammatory activation. Pharmacological inhibition of serine palmitoyl transferase (SPT) with myriocin reverses this cascade, protecting RGCs. Multi-omics integration of human glaucoma aqueous humor datasets further reveals conserved upregulation of sphingolipid biosynthetic enzymes, sphingolipid metabolites, and lipid-sensing immune effectors, offering preliminary translational clues. Collectively, our findings reveal that spatially defined immunometabolic remodeling—in which <i>Trem2</i><sup><i>+</i></sup> microglia are central—converges on sphingolipid metabolism as a druggable regulatory axis, with the TREM2-SPTLC2 interface thus emerging as a new therapeutic opportunity for retinal neurodegenerative diseases.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iMetaPub Date : 2026-08-26Epub Date: 2026-06-09DOI: 10.1002/imt2.70143
Lin-An Zhang, Xuan Dong, Kai Liu, Nicolas Gonzalez, Jose Manuel Estevez, Wen-Xue Li, Xing Wang Deng, Feng Yu, Yunbi Xu
{"title":"Enviromics crosstalk between internal and external plant environments for enhanced adaptation and de novo domestication","authors":"Lin-An Zhang, Xuan Dong, Kai Liu, Nicolas Gonzalez, Jose Manuel Estevez, Wen-Xue Li, Xing Wang Deng, Feng Yu, Yunbi Xu","doi":"10.1002/imt2.70143","DOIUrl":"https://doi.org/10.1002/imt2.70143","url":null,"abstract":"<p>Climate change demands accelerated plant adaptation and <i>de novo</i> domestication. Yet current enviromics focuses disproportionately on external environments, neglecting internal dynamics—gene expression, metabolic flux, and signal transduction—within predictive envirotyping frameworks. This gap constrains plant-environment adaptation research and crop improvement. Integrating multi-scale envirotyping with plant-environment interaction networks could catalyze a paradigm shift from empirical selection to mechanism-informed design breeding. Four challenges remain: (1) constructing adaptive multi-dimensional networks, (2) engineering transgenerational epigenetic reprogramming, (3) scaling domestication pipelines, and (4) predicting adaptive trajectories. Future efforts should converge on five domains: high-throughput microprobe envirotyping arrays, spatiotemporally resolved multi-omics, decoding epigenetic memory carriers, artificial intelligence (AI)-guided genome design, and phenotype prediction models. Ultimately, advancing from multi-omics dissection and mechanistic interpretation to targeted <i>de novo</i> design will enable the precise engineering of crop adaptive responses to environmental change.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iMetaPub Date : 2026-08-26Epub Date: 2026-07-28DOI: 10.1002/imt2.70156
Chen Tu, Jie Yang, Jingyi Liao, Rongkui Hu, Yudong Feng, Di Wu, Yankai Xia, Dan Wang, Jinrong Tang, Xianzheng Yuan, Dong Zhu, Jing Wei, Li Xu, Mingkai Xu, Xuetao Guo, Jian Zhao, Qiqing Chen, Zhenming Zhang, Lianzhen Li, Yini Ma, Xiaoxu Jiang, Kai Zhang, Cheng Peng, Mengyao Li, Ning Shen, Willie J. G. M. Peijnenburg, Matthias C. Rillig, Jason C. White, Yongming Luo, Ningwei Zhao
{"title":"Exposure to micro- and nano-plastics: From human internal burden to systems-level health-risk interpretation","authors":"Chen Tu, Jie Yang, Jingyi Liao, Rongkui Hu, Yudong Feng, Di Wu, Yankai Xia, Dan Wang, Jinrong Tang, Xianzheng Yuan, Dong Zhu, Jing Wei, Li Xu, Mingkai Xu, Xuetao Guo, Jian Zhao, Qiqing Chen, Zhenming Zhang, Lianzhen Li, Yini Ma, Xiaoxu Jiang, Kai Zhang, Cheng Peng, Mengyao Li, Ning Shen, Willie J. G. M. Peijnenburg, Matthias C. Rillig, Jason C. White, Yongming Luo, Ningwei Zhao","doi":"10.1002/imt2.70156","DOIUrl":"10.1002/imt2.70156","url":null,"abstract":"<p>Micro- and nano-plastics (MNPs) can enter the human body through inhalation, ingestion, contact with consumer products, and iatrogenic routes. The clinical relevance of MNP exposure should be interpreted at three levels: barrier interaction, cellular stress, and system-level disruption, with key mechanisms including oxidative stress, mitochondrial dysfunction, and chronic inflammation.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148622497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The plant microbiome: From ecological foundations to precision microbial engineering for sustainable agriculture","authors":"Mi Wei, Tengxiang Lian, Liying Chen, Lanxiang Wang, Junjie Ye, Xiaofang Yao, Shilong Duan, Ziyu Lu, Jinji Tu, Hongfu Li, Xin-Yue Xu, Jie Zhou, Junliang He, Feiying Zhu, Paola Bonfante, Lam-Son Phan Tran, Zhiqiang Pang, Xin Zhou, Zhihui Xu, Lin Zhang, Mengcen Wang, Xiaolin Wang, Chang-Fu Tian, Yong-Xin Liu, Kai Sun, Ertao Wang, Xianan Xie","doi":"10.1002/imt2.70152","DOIUrl":"10.1002/imt2.70152","url":null,"abstract":"<p>Plants are best understood as evolutionary holobionts, in which the host and its associated microbiomes operate as an integrated unit to influence growth, health, and stress resilience. This comprehensive review synthesizes the most current knowledge of plant-associated microbiomes across key ecological compartments, including the rhizosphere, endosphere, phyllosphere, and seeds, highlighting their assembly drivers, functional mechanisms, and translational potential. We dissect the molecular foundations of rhizobial and arbuscular mycorrhizal (AM) symbioses, the plant-AM fungus-bacterium continuum, alongside emerging concepts including the aerial root mucilagesphere, phyllosphere homeostasis, and the pathobiome. We further explore host genetic, metabolic, and environmental determinants of microbiome assembly, and present cutting-edge methodologies ranging from quantitative profiling to artificial intelligence-driven synthetic community design. Finally, we outline a strategic blueprint for harnessing standardized synthetic microbiomes and precision microbiome engineering to advance sustainable agriculture. This integrative framework bridges fundamental ecology with practical applications, delineating a path toward climate-resilient crop production.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13430161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
iMetaPub Date : 2026-08-26Epub Date: 2026-06-14DOI: 10.1002/imt2.70142
Jie Qiu, Xiaojia Wang, Man Li, Jing Guo, Shipeng Ning, Yi-Zhou Gao, Xinyi Zhang, Xuli Meng, Yiding Chen, Yunxiang Zhou
{"title":"The role of human microbiota in breast cancer pathogenesis and treatment","authors":"Jie Qiu, Xiaojia Wang, Man Li, Jing Guo, Shipeng Ning, Yi-Zhou Gao, Xinyi Zhang, Xuli Meng, Yiding Chen, Yunxiang Zhou","doi":"10.1002/imt2.70142","DOIUrl":"https://doi.org/10.1002/imt2.70142","url":null,"abstract":"<p>The human microbiota contributes to breast cancer pathogenesis and treatment response through interactions involving the oral, gut, and breast microbial niches. (Left) Multi-site dysbiosis is characterized by altered microbial composition and abundance across different anatomical sites. (Middle) Microbial components and metabolites influence tumor progression and the tumor microenvironment through mechanisms including immune, metabolic, and inflammatory regulation. (Right) The microbiota and their metabolites further affect therapeutic efficacy and toxicity in immunotherapy, chemotherapy, endocrine therapy, and human epidermal growth factor receptor 2 (HER2)-targeted therapy, highlighting the translational potential of microbiota-targeted strategies in breast cancer.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Gut microbiota-mediated immune and metabolic dysregulation in coronary artery disease progression and prognosis","authors":"Honghong Liu, Siqin Feng, Lifeng Liang, Muyun Tang, Yifei Wang, Yiyang Wang, Zhiyu Zhang, Haiping Xing, Chenhong Zhang, Ran Tian, Shuyang Zhang","doi":"10.1002/imt2.70147","DOIUrl":"https://doi.org/10.1002/imt2.70147","url":null,"abstract":"<p>The gut microbiota has emerged as a metabolically active endocrine-like organ with a crucial role in coronary artery disease (CAD), yet its contribution to adverse clinical outcomes remains incompletely understood. In this prospective cohort of 319 participants, we integrated metagenomic and metabolomic profiling with longitudinal follow-up over a median of 1.85 years. Fecal microbiota transplantation from patients with CAD transmitted susceptibility to atherosclerosis in antibiotic-treated <i>ApoE</i><sup>−/−</sup> mice, accompanied by microbiota-induced vascular inflammation mediated through LPS–TLR4 signaling. Gut microbiota-derived aromatic amino acid metabolism was associated with thrombotic risk and major adverse cardiac events (MACE). Machine learning identified gut microbial features that improved prospective prediction of MACE. Together, these findings implicate the gut microbiome in CAD progression and support the development of microbiome-based strategies for cardiovascular risk prediction and prevention.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"5 4","pages":""},"PeriodicalIF":44.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.70147","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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