iMeta最新文献

{"title":"MASH-Ocean 1.0: Interactive platform for investigating microbial diversity, function, and biogeography with marine metagenomic data","authors":"Yinzhao Wang,&nbsp;Liuyang Li,&nbsp;Qiang Li,&nbsp;Yaoxun Hu,&nbsp;Wenjie Li,&nbsp;Zhile Wu,&nbsp;Hungchia Huang,&nbsp;Zhenbo Lv,&nbsp;Wan Liu,&nbsp;Ruifang Cao,&nbsp;Guoping Zhao,&nbsp;Fengping Wang,&nbsp;Guoqing Zhang","doi":"10.1002/imt2.201","DOIUrl":"10.1002/imt2.201","url":null,"abstract":"<p>A large number of oceanic metagenomic data and environmental metadata have been published. However, most studies focused on limited ecosystems using different analysis tools, making it challenging to integrate these data into robust results and comprehensive global understanding of marine microbiome. Here, we constructed a systematic and quantitative analysis platform, the Microbiome Atlas/Sino-Hydrosphere for Ocean Ecosystem (MASH-Ocean: https://www.biosino.org/mash-ocean/), by integrating global marine metagenomic data and a unified data processing flow. MASH-Ocean 1.0 comprises 2147 metagenomic samples with five analysis modules: sample view, diversity, function, biogeography, and interaction network. This platform provides convenient and stable support for researchers in microbiology, environmental science, and biogeochemistry, to ensure the integration of omics data generated from hydrosphere ecosystems, to bridge the gap between elusive omics data and biological, ecological, and geological discovery, ultimately to foster the formation of a comprehensive atlas for aquatic environments.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141123596","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":"Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition","authors":"Lingyan Ma,&nbsp;Wentao Lyu,&nbsp;Tao Zeng,&nbsp;Wen Wang,&nbsp;Qu Chen,&nbsp;Jiangchao Zhao,&nbsp;Guolong Zhang,&nbsp;Lizhi Lu,&nbsp;Hua Yang,&nbsp;Yingping Xiao","doi":"10.1002/imt2.198","DOIUrl":"10.1002/imt2.198","url":null,"abstract":"<p>The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140978338","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":"Understanding host immune responses in Clostridioides difficile infection: Implications for pathogenesis and immunotherapy","authors":"Lamei Wang,&nbsp;Javier A. Villafuerte Gálvez,&nbsp;Christina Lee,&nbsp;Shengru Wu,&nbsp;Ciaran P. Kelly,&nbsp;Xinhua Chen,&nbsp;Yangchun Cao","doi":"10.1002/imt2.200","DOIUrl":"10.1002/imt2.200","url":null,"abstract":"<p><i>Clostridioides difficile</i> (<i>C. difficile</i>) is the predominant causative agent of nosocomial diarrhea worldwide. Infection with <i>C. difficile</i> occurs due to the secretion of large glycosylating toxin proteins, which can lead to toxic megacolon or mortality in susceptible hosts. A critical aspect of <i>C. difficile's</i> biology is its ability to persist asymptomatically within the human host. Individuals harboring asymptomatic colonization or experiencing a single episode of <i>C. difficile</i> infection (CDI) without recurrence exhibit heightened immune responses compared to symptomatic counterparts. The significance of these immune responses cannot be overstated, as they play critical roles in the development, progression, prognosis, and outcomes of CDI. Nonetheless, our current comprehension of the immune responses implicated in CDI remains limited. Therefore, further investigation is imperative to elucidate their underlying mechanisms. This review explores recent advancements in comprehending CDI pathogenesis and how the host immune system response influences disease progression and severity, aiming to enhance our capacity to develop immunotherapy-based treatments for CDI.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.200","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140989447","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":"Cardiovascular disease therapeutics via engineered oral microbiota: Applications and perspective","authors":"Wenyu Zhen,&nbsp;Zifei Wang,&nbsp;Qing Wang,&nbsp;Wansu Sun,&nbsp;Rui Wang,&nbsp;Wenhao Zhang,&nbsp;Yulong Zhang,&nbsp;Wengang Qin,&nbsp;Bang Li,&nbsp;Qingqing Wang,&nbsp;Biao Hong,&nbsp;Yicheng Yang,&nbsp;Jing Xu,&nbsp;Siyu Ma,&nbsp;Ming Da,&nbsp;Linfei Feng,&nbsp;Xiaodong Zang,&nbsp;Xuming Mo,&nbsp;Xiaoyu Sun,&nbsp;Mingyue Wu,&nbsp;Junji Xu,&nbsp;Jianguang Xu,&nbsp;Yuan Huang,&nbsp;Hengguo Zhang","doi":"10.1002/imt2.197","DOIUrl":"10.1002/imt2.197","url":null,"abstract":"<p>Engineering bacteria are considered as a potential treatment for cardiovascular diseases and related risk factors. Oral bacteria are closely related to the occurrence and development of cardiovascular diseases, and their engineering has broad prospects and potential in the treatment of cardiovascular diseases. Oral pathogenic bacteria undergo protein and genetic engineering, including the incorporation of exogenous plasmids to yield therapeutic effects; genetically engineered oral probiotics can be harnessed to secrete cytokines and reactive oxygen species, offering novel therapeutic avenues for cardiovascular diseases.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.197","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140996777","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":"A new evaluation system for drug–microbiota interactions","authors":"Tian-Hao Liu,&nbsp;Chen-Yang Zhang,&nbsp;Hang Zhang,&nbsp;Jing Jin,&nbsp;Xue Li,&nbsp;Shi-Qiang Liang,&nbsp;Yu-Zheng Xue,&nbsp;Feng-Lai Yuan,&nbsp;Ya-Hong Zhou,&nbsp;Xiu-Wu Bian,&nbsp;Hong Wei","doi":"10.1002/imt2.199","DOIUrl":"10.1002/imt2.199","url":null,"abstract":"<p>The drug response phenotype is determined by a combination of genetic and environmental factors. The high clinical conversion failure rate of gene-targeted drugs might be attributed to the lack of emphasis on environmental factors and the inherent individual variability in drug response (IVDR). Current evidence suggests that environmental variables, rather than the disease itself, are the primary determinants of both gut microbiota composition and drug metabolism. Additionally, individual differences in gut microbiota create a unique metabolic environment that influences the in vivo processes underlying drug absorption, distribution, metabolism, and excretion (ADME). Here, we discuss how gut microbiota, shaped by both genetic and environmental factors, affects the host's ADME microenvironment within a new evaluation system for drug–microbiota interactions. Furthermore, we propose a new top-down research approach to investigate the intricate nature of drug–microbiota interactions in vivo. This approach utilizes germ-free animal models, providing foundation for the development of a new evaluation system for drug–microbiota interactions.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.199","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141004407","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":"Intestinal linoleic acid contributes to the protective effects of Akkermansia muciniphila against Listeria monocytogenes infection in mice","authors":"Tong Jin,&nbsp;Yingying Zhang,&nbsp;Yanpeng Yang,&nbsp;Yue Teng,&nbsp;Chunhong Yan,&nbsp;Zhongguo Shan,&nbsp;Jianghong Meng,&nbsp;Xiaodong Xia","doi":"10.1002/imt2.196","DOIUrl":"https://doi.org/10.1002/imt2.196","url":null,"abstract":"<p><i>Akkermansia muciniphila</i> pretreatment mitigated <i>Listeria monocytogenes</i> infection in mice. <i>A. muciniphila</i> improved gut microbiota disturbed by <i>L. monocytogenes</i> infection and significantly increased the level of intestinal linoleic acid in mice. Linoleic acid strengthened the intestinal epithelial barrier and reduced pathogen translocation partly by regulating NF-κB/MLCK pathway in a GPR40-dependent manner.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425132","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":"GutUDB: A comprehensive multiomics database for intestinal diseases","authors":"Yi Bao,&nbsp;Yaxin Chen,&nbsp;Lizhu Lin,&nbsp;Jingyi Li,&nbsp;Xinli Liu,&nbsp;Gang Wang,&nbsp;Yueqi Li,&nbsp;Yao Lin,&nbsp;Yajing Chen,&nbsp;Lijuan Zhou,&nbsp;Yawen Qi,&nbsp;Yufang Xie,&nbsp;Zhenrui Lin,&nbsp;Zhe Sun,&nbsp;Yuwen Fan,&nbsp;Jinjing Jiang,&nbsp;Feiyu Zhang,&nbsp;Hubin Chen,&nbsp;Jiemei Chu,&nbsp;Jiegang Huang,&nbsp;Xuena Chen,&nbsp;Hao Liang,&nbsp;Shuaiyi Liang,&nbsp;Sanqi An","doi":"10.1002/imt2.195","DOIUrl":"https://doi.org/10.1002/imt2.195","url":null,"abstract":"<p>Gut Universe Database (GutUDB) provides a comprehensive, systematic, and practical platform for researchers, and is dedicated to the management, analysis, and visualization of knowledge related to intestinal diseases. Based on this database, eight major categories of omics data analyses are carried out to explore the genotype-phenotype characteristics of a certain intestinal disease. The first tool for comprehensive omics data research on intestinal diseases will help each researcher better understand intestinal diseases.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425131","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":"Long-term nitrogen input reduces soil bacterial network complexity by shifts in life history strategy in temperate grassland","authors":"Chao Wang,&nbsp;Ziyue Shi,&nbsp;Aogui Li,&nbsp;Tianyi Geng,&nbsp;Lingli Liu,&nbsp;Weixing Liu","doi":"10.1002/imt2.194","DOIUrl":"10.1002/imt2.194","url":null,"abstract":"<p>We investigated soil bacterial and fungal communities, constructed co-occurrence networks, and estimated bacterial traits along a gradient of nitrogen (N) input. The results showed that soil bacterial co-occurrence networks complexity decreased with increasing N input. The ratio of negative to positive cohesion decreased with increasing N input, suggesting the declined competitive but strengthened cooperative interactions. However, soil fungal network complexity did not change under N enrichment. In addition, N input stimulated the copiotroph/oligotroph ratio, ribosomal RNA operon (<i>rrn</i>) copy number, and guanine-cytosine (GC) content of soil bacteria, shifting bacterial life history strategy toward copiotroph with increased <i>r</i>-/<i>K</i>-strategy ratio. Piecewise structural equation modeling results further revealed that the reduction in bacterial co-occurrence network complexity was directly regulated by the increased bacterial <i>r</i>-/<i>K</i>-strategy ratio, rather than reduced bacterial richness. Our study reveals the mechanisms through which microbial traits regulate interactions and shape co-occurrence networks under global changes.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140699884","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":"Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams","authors":"Mei Yang,&nbsp;Tong Chen,&nbsp;Yong-Xin Liu,&nbsp;Luqi Huang","doi":"10.1002/imt2.184","DOIUrl":"https://doi.org/10.1002/imt2.184","url":null,"abstract":"<p>Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141424894","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":"Clinical features and molecular landscape of cuproptosis signature-related molecular subtype in gastric cancer","authors":"Wei Chong,&nbsp;Huicheng Ren,&nbsp;Hao Chen,&nbsp;Kang Xu,&nbsp;Xingyu Zhu,&nbsp;Yuan Liu,&nbsp;Yaodong Sang,&nbsp;Han Li,&nbsp;Jin Liu,&nbsp;Chunshui Ye,&nbsp;Liang Shang,&nbsp;Changqing Jing,&nbsp;Leping Li","doi":"10.1002/imt2.190","DOIUrl":"10.1002/imt2.190","url":null,"abstract":"<p>Recent studies have highlighted the biological significance of cuproptosis in disease occurrence and development. However, it remains unclear whether cuproptosis signaling also has potential impacts on tumor initiation and prognosis of gastric cancer (GC). In this study, 16 cuproptosis-related genes (CRGs) transcriptional profiles were harnessed to perform the regularized latent variable model-based clustering in GC. A cuproptosis signature risk scoring (CSRS) scheme, based on a weighted sum of principle components of the CRGs, was used to evaluate the prognosis and risk of individual tumors of GC. Four distinct cuproptosis signature-based clusters, characterized by differential expression patterns of CRGs, were identified among 1136 GC samples across three independent databases. The four clusters were also associated with different clinical outcomes and tumor immune contexture. Based on the CSRS, GC patients can be divided into CSRS-High and CSRS-Low subtypes. We found that <i>DBT, MTF1</i>, and <i>ATP7A</i> were significantly elevated in the CSRS-High subtype, while <i>SLC31A1, GCSH, LIAS, DLAT, FDX1, DLD</i>, and <i>PDHA1</i> were increased in the CSRS-Low subtype. Patients with CSRS-Low score were characterized by prolonged survival time. Further analysis indicated that CSRS-Low score also correlated with greater tumor mutation burden (TMB) and higher mutation rates of significantly mutated genes (SMG) in GC. In addition, the CSRS-High subtype harbored more significantly amplified focal regions related to tumorigenesis (<i>3q27.1, 12p12.1, 11q13.3</i>, etc.) than the CSRS-Low tumors. Drug sensitivity analyses revealed the potential compounds for the treatment of gastric cancer with CSRS-High score, which were experimentally validated using GC cells. This study highlights that cuproptosis signature-based subtyping is significantly associated with different clinical features and molecular landscape of GC. Quantitative evaluation of the CSRS of individual tumors will strengthen our understanding of the occurrence and development of cuproptosis and the treatment progress of GC.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.190","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140735903","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}