iMetaOmics最新文献

{"title":"Majorbio Cloud: An integrated platform for single-omics and integrated multi-omics analysis of microbiome and metabolome.","authors":"Jianhua Zhao, Linmeng Liu, Bing Yang, Mengxi Li, Junbiao Zhang, Jichen Han, Xiaodan Li, Yan Wang, Shaobing Du, Qianhui Han, Linna Zhang, Wenjuan Sun, Hao Gao, Yachen Dong, Huasheng Huang, Xianglin Zhang, Kegang Yu","doi":"10.1002/imo2.70111","DOIUrl":"10.1002/imo2.70111","url":null,"abstract":"<p><p>Advances in sequencing and mass spectrometry have propelled life sciences into the multi-omics era. Metabolomics and microbiomics are widely applied across various research fields, yet massive data analysis faces challenges like limited tool functionality and high technical barriers. The Majorbio Cloud Platform addresses these pain points by establishing four integrated workflows: Untargeted metabolomics, targeted metabolomics, microbiomics, and microbiome-metabolome integrated analysis, enabling one-stop analysis from single-omics to multi-omics correlation. In a real gut microbiome-metabolome case study, the platform pinpointed core differential microbes and characteristic metabolites, and further annotated functional pathways underlying host phenotypic divergence, demonstrating its reliability for mining biological mechanisms. The platform caters to both novice and experienced researchers with dual-parameter modes (default/customizable), multi-user collaboration, standardized pipelines, advanced analytical tools, and one-click color customization. By simplifying complex analytical procedures and reducing reliance on specialized programming skills, it offers a standardized, reproducible solution for multi-omics data analysis in related fields.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70111"},"PeriodicalIF":0.0,"publicationDate":"2026-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218045","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":"Pioneering the canine model in microbiota-gut-brain research for social and affective disorders.","authors":"Yun Yu, Qiuhan Wen, Xiaoyang Wang, Mengyu Song, Tifei Yuan, Feilong Deng, Jianmin Chai, Ying Li, Ya-Ping Zhang","doi":"10.1002/imo2.70113","DOIUrl":"10.1002/imo2.70113","url":null,"abstract":"<p><p>This commentary highlights the translational potential of canine models in investigating the microbiota-gut-brain (MGB) axis, focusing on their relevance to human social cognition and affective disorders, including major depressive disorder and autism spectrum disorder. While traditional rodent models provide foundational knowledge, the unique socio-behavioral complexity of dogs offers a potential bridge to study the shared neuroendocrine and microbial substrates underlying human psychopathology. This commentary outlines the promising avenues for canine-based research while critically addressing the practical limitations inherent in generalizing these findings to human populations, including genetic heterogeneity, standardization challenges, and ethical considerations. We propose a phased research pathway incorporating fecal microbiota transplantation and neurobehavioral phenotyping to define a clear trajectory for future translational research. Leveraging this canine platform creates a One Health paradigm, delivering mutual diagnostic and therapeutic advancements for both human and veterinary medicine, with applications for conditions such as anxiety and gastrointestinal disorders.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70113"},"PeriodicalIF":0.0,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218101","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":"Microbial ecological memory of recurrent drought enhances host stress tolerance through enrichment of plant-beneficial bacteria.","authors":"Chengguang Xing, Dandan Zhou, Dongwei Hou, Chunyi Lei, Zhiwei Liu, Jinhui Liu, Chaojian Hu, Jinye Liu, Shuzhen Huang, Yong Huo, Mingrui Zhou, Weiqiu Liu","doi":"10.1002/imo2.70110","DOIUrl":"10.1002/imo2.70110","url":null,"abstract":"<p><p>Recurrent desiccation induced niche-specific microbial ecological memory in the green part of <i>Calohypnum plumiforme</i>, marked by enrichment of plant-beneficial bacteria, especially <i>Methylobacterium</i> and <i>Sphingomonas</i>, and functional shifts toward symbiosis and stress protection, potentially enhancing host tolerance within a \"holobiont ecology memory\" framework.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70110"},"PeriodicalIF":0.0,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218040","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":"Host-specific and deterministic microbiome assembly in major coleopteran stored-grain pests.","authors":"Abrar Muhammad, Xiaoqiang Shen, Lichao Chen, Enhui Guo, Huarui Zhang, Xiaoyu Lei, Chao Sun, Jianhua Lv, Yongqi Shao","doi":"10.1002/imo2.70109","DOIUrl":"10.1002/imo2.70109","url":null,"abstract":"<p><p>Dual DNA- and RNA-based sequencing profiled the microbiomes of five major coleopteran stored-grain pests and their wheat flour substrate. The microbiomes differed significantly among hosts and from flour, yet 11 core bacterial and 9 core fungal taxa were shared across hosts. RNA data revealed host-specific active microbiota. Deterministic processes dominated community assembly, exceeding 90% in <i>Rhyzopertha dominica</i> and <i>Oryzaephilus surinamensis</i>. Homogeneous selection identified eight conserved bacterial clades. Although microbiomes were strongly host-specific, they showed no significant correlation with host phylogeny, indicating that environmental filtering and deterministic selection, rather than evolutionary relatedness, are the dominant forces shaping these pest-associated communities.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70109"},"PeriodicalIF":0.0,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218026","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":"Metagenomic mining of environmental resistomes: Comparative performance of deep learning and alignment-based annotation methods.","authors":"Joeselle M Serrana, Francisco J A Nascimento, Malte Posselt","doi":"10.1002/imo2.70107","DOIUrl":"10.1002/imo2.70107","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) in marine environments poses intricate challenges due to the ecological complexity of microbial communities and environmental gradients. This study compares various antimicrobial resistance gene (ARG) annotation tools and databases, focusing on deep learning approaches versus traditional alignment-based methods, to evaluate their effectiveness in profiling the resistome of a complex marine ecosystem. Our report not only highlights the utility of deep learning methods for environmental applications but also proposes pathways for future improvements that can bridge the gap between comprehensive detection and clinically relevant risk interpretation.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 2","pages":"e70107"},"PeriodicalIF":0.0,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218078","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":"Sexual dimorphism in hormone-gut microbiome associations across reproductive states in wild giant pandas.","authors":"Qinlong Dai, Xinyuan Cui, Chenyi Gao, Xiaoxiao Tang, Kaizhi Wen, Minhui Shi, Chen Zhang, Yue Liu, Xinru Yang, Qiuyu Huang, Lifeng Zhu","doi":"10.1002/imo2.70108","DOIUrl":"10.1002/imo2.70108","url":null,"abstract":"<p><p>Gut microbiota-host endocrine interactions in wild mammals remain poorly understood. Giant pandas experience seasonal dietary shifts and constrained annual reproduction, offering an ideal model to investigate microbiome-endocrine coupling. We integrated fecal hormone profiling, microsatellite-based individual identification, and gut microbiome sequencing in wild giant pandas. Microbial diversity and composition varied seasonally, with α diversity peaking during bamboo shoot-feeding. Hormonal dynamics followed predictable patterns: elevated estrogen during estrus, sustained progesterone post-estrus, and higher cortisol during leaf/stem-feeding periods. Hormone levels significantly correlated with microbial taxa and diversity, indicating coordinated microbiome-endocrine dynamics. Notably, microbiome-hormone coupling was significant in males but not in females, and males exhibited greater hormonal and microbial variability. Our findings demonstrate seasonal restructuring of gut microbiome and endocrine profiles in wild giant pandas with sex-dependent coupling, providing an integrated framework for non-invasive conservation monitoring.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70108"},"PeriodicalIF":0.0,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218093","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":"Gene expression signatures from single-cell transcriptomics predict Sjögren's syndrome.","authors":"Shumin Cheng, Ling Yan, Yilin Wu, Yan Li, Ziheng Ye, Zhen Zhang, Yi Zhang, Jingyun Ma, Yuhong Liang, Zhaofan Luo, Huacheng Wang, Meili Gao, Chao Qin, Ke Zhu, Yun Leng, Kamran Ullah, Jun Liang, Haiyan Yan, Guan Yang, Yingqian Mo, Bihui Huang","doi":"10.1002/imo2.70106","DOIUrl":"10.1002/imo2.70106","url":null,"abstract":"<p><p>Sjögren's syndrome (SjS) is a systemic autoimmune disorder characterized by lymphocytic infiltration of exocrine glands, leading to dry eyes and mouth. While previous genome-wide association studies (GWAS) and transcriptomic analyses have identified genes associated with SjS, predictive models based on single-cell resolution are limited. In this study, single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) of SjS patients were analyzed to map immune cell alterations linked to the disease. Compared with healthy controls, SjS patients displayed decreased proportions of naïve <i>CD8</i> ⁺ T cells and <i>Helios FOXP3</i> ^<i>lo</i> <i>CD4</i> ⁺ Tregs, alongside increased frequencies of <i>CTLA</i>-4⁺ <i>CD8</i> ⁺ inhibitory T cells and <i>TRDC</i> γδ T cells. Using machine learning, a predictive model for SjS diagnosis was developed based on a 12-gene signature (SjS. Sig: <i>GIMAP7</i>, <i>PSMB8</i>, <i>CD27</i>, <i>CCR7</i>, <i>TAGAP</i>, <i>UQCR10</i>, <i>HCLS1</i>, <i>LCK</i>, <i>TNFAIP3</i>, <i>ISG15</i>, <i>GIMAP4</i>, and <i>HLA</i>-<i>DRB1</i>), which effectively differentiated patients from healthy individuals. Key genes such as <i>CD27</i>, <i>PSMB8</i>, <i>HCLS1</i>, <i>LCK</i>, <i>UQCR10</i>, and <i>GIMAP4</i> were validated in clinical samples through flow cytometry and real-time quantitative PCR. These findings provide insights into the immune landscape of SjS at a single-cell resolution and propose a reliable molecular signature for diagnosis and immune monitoring.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 3","pages":"e70106"},"PeriodicalIF":0.0,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217943","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":"Diversity and distribution of bacterial phytases.","authors":"Michael Weber, Lena-Sophie Paul, Thilo M Fuchs","doi":"10.1002/imo2.70104","DOIUrl":"10.1002/imo2.70104","url":null,"abstract":"<p><p><b>Phytases:</b> The stepwise dephosphorylation of phytate is catalyzed by phytases, a group of enzymes found mainly among bacteria and plants. <b>Bacterial potential:</b> We identified an unexpectedly widespread and previously underappreciated bacterial potential for phytate dephosphorylation, suggesting that microbial phytases play crucial roles in the environmental and host-associated phosphorus flux. <b>Diversity:</b> We analyzed 115,379 validated bacterial genomes to resolve the taxonomic distribution and diversity of potentially phytase-producing bacterial species, and identified phytase genes in 6281 out of 25,105 species (25%). <b>Prevalence:</b> Phytases were predominantly found in members of the phyla Pseudomonadota, Bacteroidota, and Cyanobacteriota, but were comparatively rare in Bacillota and Actinomycetota, with alkaline β-propeller phytases as the most prevalent and widespread category.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 2","pages":"e70104"},"PeriodicalIF":0.0,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218104","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":"Integrated high-throughput phenomics and transcriptomics uncover the transcriptional mechanisms underlying rice responses to elevated CO₂ concentration and cadmium stress.","authors":"Weijun Guo, Hanlin Liu, Dongwei Li, Shang Xie, Yichao Mao, Liwen Yang, Cong Li, Weixuan Wang, Jian Tian, Xiaofeng Gu, Li Pu","doi":"10.1002/imo2.70100","DOIUrl":"10.1002/imo2.70100","url":null,"abstract":"<p><p>Developing crop varieties with reduced cadmium (Cd) accumulation under elevated carbon dioxide (eCO₂) is a major global challenge. Identifying hub genes and elucidating the transcriptional mechanisms governing Cd stress and eCO₂ responses requires integrated, multi-tissue omics approaches. Here, we conducted high-throughput phenotyping of the rice cultivar Nipponbare across six key developmental stages under Cd stress and three eCO₂ concentrations. Image-based traits revealed shared and distinct phenotypic responses to these stresses. Multi-tissue transcriptome analyses showed that the differentially expressed genes (DEGs) and hormone-related genes exhibited a similar expression pattern under Cd and eCO₂. We further constructed an integrative co-expression network and identified five stress-responsive subnetworks. Among these, <i>Multiple Stress Responsive Gene 3</i> (<i>OsMSR3</i>) emerged as a hub gene, with its haplotype 2 (Hap2) frequency decreasing from low- to high-latitude regions and from southern to northeastern China, mirroring the geographic distribution of Cd-contaminated soils. Collectively, our study reveals a transcriptional regulatory network underlying rice responses to Cd and eCO₂ stresses, providing mechanistic insights and valuable genetic resources for future molecular breeding of low-Cd accumulating rice varieties adapted to constant rising CO₂ levels.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 2","pages":"e70100"},"PeriodicalIF":0.0,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218068","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":"Changes in the gut microbiome during fasting-induced molting and its effects on gut-liver function.","authors":"Hao Zhang, Zhixuan Luo, Jun Zhang, Chenxu Wang, Yadong Tian, Donghua Li, Yujie Guo, Yanhua Zhang, Wenting Li, Yujie Gong, Xiangtao Kang, Ruirui Jiang","doi":"10.1002/imo2.70103","DOIUrl":"10.1002/imo2.70103","url":null,"abstract":"<p><p>Fasting-induced molting (FIM) rejuvenates the laying cycle in hens; however, the fasting process may result in intestinal dysbiosis, which compromises host immunity and disrupts the intestine-liver function. Consequently, investigating the changes in gut microbiota during FIM and its impacts on gut-liver metabolic homeostasis is crucial for enhancing the efficiency of FIM in laying hens. Here, a total of 90 laying hens, aged 60 weeks, were selected for the FIM. Samples were collected at four time points: the day before fasting, the 15th day of fasting, the 5th day of refeeding, and the 47th day of refeeding. Metagenomic sequencing and non-targeted metabolomics were employed to investigate the roles of the gut microbiota and metabolites in the remodeling of gut-liver function, focusing on intestinal injury-repair mechanisms and changes in liver function. During the fasting period, the abundance of harmful microbiota and metabolites increase, leading to intestinal injury. This process activates the TGF-beta signaling pathway, promoting intestinal stem cell proliferation. Simultaneously, liver function dysfunction as evidenced by elevated bile acid levels in the liver and serum and activation of the non-classical bile acid synthesis pathway. During the refeeding period, the previously observed effects were reversed, leading to the remodeling of the intestinal microbiota and gut-liver function. We identified key microorganisms (<i>Liquorilactobacillus mali</i> and <i>Tissierellia</i> bacterium KA00581) and functional metabolites (d-Panthenol and 3-hydroxyanthranilic acid (3-HAA)) involved in intestinal-liver function during FIM. Notably, d-Panthenol promotes chicken small intestinal organoid branching and growth, enhances barrier function, and reduces inflammation. Our study underscores the role of gut microbiota in gut-liver injury during FIM in laying hens, suggesting potential probiotic- or metabolite-based interventions to mitigate gut-liver injury and facilitate recovery.</p>","PeriodicalId":521007,"journal":{"name":"iMetaOmics","volume":"3 2","pages":"e70103"},"PeriodicalIF":0.0,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13674437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149218077","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}