iMeta最新文献

{"title":"Correction to “Lepidium meyenii Walp (Maca)-derived extracellular vesicles ameliorate depression by promoting 5-HT synthesis via the modulation of gut–brain axis”","authors":"","doi":"10.1002/imt2.259","DOIUrl":"10.1002/imt2.259","url":null,"abstract":"<p>In Hong et al. [<span>1</span>], following details should have been corrected.</p><p>1. In page 6, “We also investigated the effect of Maca-EVs on microbial diversity and found that microbial richness as indicated by the Faith-pd and Observed features index was higher in the Maca-EVs groups (Control+Maca-EVs and UCMS+Maca-EVs).” was incorrect.</p><p>This should be: “We also investigated the effect of Maca-EVs on microbial diversity and found that microbial richness as indicated by the Faith-pd and Observed features index was lower in the Maca-EVs groups (Control+Maca-EVs and UCMS+Maca-EVs).”</p><p>2. In page 6, the sentence “Only the Faith pd index in Control + Maca EVs group was significantly lower than that in the Control group (<i>p</i> &lt; 0.05, figure 3D).” should be deleted.</p><p>3. In Figure 4, page 8 of the article, “(F) Reciprocal interactions between altered gut bacteria and serum metabolites identified by a co-occurrence network based on Spearman correlation analysis in pos mode.” was incorrect.</p><p>This should be: “(F) Reciprocal interactions between altered gut bacteria and metabolites identified by a co-occurrence network based on Spearman correlation analysis in pos mode.”</p><p>We apologize for these errors.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916250","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":"EXPRESSION OF CONCERN: Intratumoral Microbiota is Associated with Prognosis in Patients with Adrenocortical Carcinoma","authors":"","doi":"10.1002/imt2.255","DOIUrl":"10.1002/imt2.255","url":null,"abstract":"<p><b>EXPRESSION OF CONCERN</b>: Y. Li, D. Zhang, M. Wang, H. Jiang, C. Feng, and Y.–X. Li, “Intratumoral Microbiota is Associated with Prognosis in Patients with Adrenocortical Carcinoma,” <i>iMeta</i> 2, no. 2 (2023): e102, https://doi.org/10.1002/imt2.102.</p><p>This Expression of Concern is for the above article, published online on 05 April 2023 in Wiley Online Library (wileyonlinelibrary.com), and has been published by agreement between the journal Editors-in-Chief, Shuang-Jiang Liu and Jingyuan Fu; iMeta Science; and John Wiley &amp; Sons Australia, Ltd.</p><p>The above article utilized data partially derived from Poore et al. [<span>1</span>], which was later retracted due to data analysis errors [<span>2</span>]. In light of this retraction and the resulting uncertainty regarding the data, readers are advised to interpret the results of the present study with caution.</p><p>The journal team and the publisher are currently investigating the concerns to determine whether it affects the conclusions of the article. The authors have agreed to re-analyze their data. In the meantime, the journal has decided to issue an Expression of Concern to inform and alert the readers.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916338","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":"Polyploidy drives autophagy to participate in plant-specific functions","authors":"Moyang Liu,&nbsp;Ming Yang,&nbsp;Heng Liang,&nbsp;Bote Luo,&nbsp;Junjie Deng,&nbsp;Lingyan Cao,&nbsp;Daojun Zheng,&nbsp;Cheng Chen","doi":"10.1002/imt2.252","DOIUrl":"10.1002/imt2.252","url":null,"abstract":"<p>Polyploidization promotes the functional diversification of autophagy in plants, expanding autophagy-associated genes (AAGs) to support processes like chloroplast division and flowering. Analysis of 92,967 AAGs in <i>Arabidopsis thaliana</i>, <i>Solanum lycopersicum, Camellia oleifera</i>, and 74 other plant species shows that 45.69% of AAGs are polyploidy-related, highlighting polyploidy's role in linking autophagy to plant-specific functions.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916344","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 analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota","authors":"Zheng-Han Lian,&nbsp;Nimaichand Salam,&nbsp;Sha Tan,&nbsp;Yang Yuan,&nbsp;Meng-Meng Li,&nbsp;Yu-Xian Li,&nbsp;Ze-Tao Liu,&nbsp;Chao-Jian Hu,&nbsp;Ai-Ping Lv,&nbsp;Yu-Ting OuYang,&nbsp;Cai-Yu Lu,&nbsp;Jing-Yi Zhang,&nbsp;Ying Chen,&nbsp;Le-Bin Chen,&nbsp;Zhen-Hao Luo,&nbsp;Bin Ma,&nbsp;Zheng-Shuang Hua,&nbsp;Jian-Yu Jiao,&nbsp;Wen-Jun Li,&nbsp;Lan Liu","doi":"10.1002/imt2.249","DOIUrl":"10.1002/imt2.249","url":null,"abstract":"<p><i>Zhuqueibacterota</i> is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the <i>Fibrobacterota</i>-<i>Chlorobiota</i>-<i>Bacteroidota</i> superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order <i>Zhuqueibacterales</i> utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916341","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":"Targeting SLC7A11/xCT improves radiofrequency ablation efficacy of HCC by dendritic cells mediated anti-tumor immune response","authors":"Yuzhao Jin,&nbsp;Songhua Cai,&nbsp;Yang Zhou,&nbsp;Dandan Guo,&nbsp;Yuzhen Zeng,&nbsp;Wangting Xu,&nbsp;Yiting Sun,&nbsp;Yueli Shi,&nbsp;Zhiyong Xu,&nbsp;Zaoqu Liu,&nbsp;Peng Luo,&nbsp;Zhao Huang,&nbsp;Bufu Tang","doi":"10.1002/imt2.248","DOIUrl":"10.1002/imt2.248","url":null,"abstract":"<p>After RFA treatment in patients with liver cancer, the expression of <i>SLC7A11</i>/xCT and the proportion of DCs in the TME were significantly increased. <i>SLC7A11</i>/xCT is a poor prognostic marker for liver cancer and is mainly expressed in DCs in the TME. Targeting xCT in DCs combined with RFA significantly enhances anti-tumor immunity, suppressing tumor growth and offering a promising strategy for improved therapeutic outcomes in liver cancer.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916380","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 comprehensive atlas of endogenous peptides in maize","authors":"Usman Ali,&nbsp;Lei Tian,&nbsp;Ruihong Tang,&nbsp;Shunxi Wang,&nbsp;Weiwei Luo,&nbsp;Shanshan Liu,&nbsp;Jinghua Zhang,&nbsp;Liuji Wu","doi":"10.1002/imt2.247","DOIUrl":"10.1002/imt2.247","url":null,"abstract":"<p>In this study, we present a comprehensive peptidomic atlas of 13 maize tissues, covering both vegetative and reproductive phases. Using a three-frame translation of canonical coding sequences, we identified 6100 nonredundant endogenous peptides, significantly expanding the known plant peptide repertoire. By integrating peptidomic coexpression profiles with previously reported proteomic profiles, we found that the peptide abundance did not consistently correlate with the abundance of their source proteins, suggesting the presence of complex regulatory mechanisms. This integrated peptidomic and proteomic map can serve as a valuable resource for exploring the functional roles of endogenous peptides in maize development and facilitates the investigation of the functional relationship among genes, peptides, and proteins across various biological contexts.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916078","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":"MetOrigin 2.0: Advancing the discovery of microbial metabolites and their origins","authors":"Gang Yu,&nbsp;Cuifang Xu,&nbsp;Xiaoyan Wang,&nbsp;Feng Ju,&nbsp;Junfen Fu,&nbsp;Yan Ni","doi":"10.1002/imt2.246","DOIUrl":"10.1002/imt2.246","url":null,"abstract":"<p>First introduced in 2021, MetOrigin has quickly established itself as a powerful web server to distinguish microbial metabolites and identify the bacteria responsible for specific metabolic processes. Building on the growing understanding of the interplay between the microbiome and metabolome, and in response to user feedback, MetOrigin has undergone a significant upgrade to version 2.0. This enhanced version incorporates three new modules: (1) Quick search module that facilitates the rapid identification of bacteria associated with a particular metabolite; (2) Orthology analysis module that links metabolic enzyme genes with their corresponding bacteria; (3) Mediation analysis module that investigates potential causal relationships among bacteria, metabolites, and phenotypes, highlighting the mediating role of metabolites. Additionally, the backend MetOrigin database has been updated with the latest data from seven public databases (KEGG, HMDB, BIGG, ChEBI, FoodDB, Drugbank, and T3DB), with expanded coverage of 210,732 metabolites, each linked to its source organism. MetOrigin 2.0 is freely accessible at http://metorigin.met-bioinformatics.cn.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916342","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 crop mined phosphorus nutrition via modifying root traits and rhizosphere micro-food web to meet the increased growth demand under elevated CO2","authors":"Na Zhou,&nbsp;Xue Han,&nbsp;Ning Hu,&nbsp;Shuo Han,&nbsp;Meng Yuan,&nbsp;Zhongfang Li,&nbsp;Sujuan Wang,&nbsp;Yingchun Li,&nbsp;Hongbo Li,&nbsp;Zed Rengel,&nbsp;Yuji Jiang,&nbsp;Yilai Lou","doi":"10.1002/imt2.245","DOIUrl":"10.1002/imt2.245","url":null,"abstract":"<p>Elevated CO₂ (eCO₂) stimulates productivity and nutrient demand of crops. Thus, comprehensively understanding the crop phosphorus (P) acquisition strategy is critical for sustaining agriculture to combat climate changes. Here, wheat (<i>Triticum aestivum</i> L) was planted in field in the eCO₂ (550 µmol mol⁻¹) and ambient CO₂ (aCO₂, 415 µmol mol⁻¹) environments. We assessed the soil P fractions, root morphological and physiological traits and multitrophic microbiota [including arbuscular mycorrhizal fungi (AMF), alkaline phosphomonoesterase (ALP)-producing bacteria, protozoa, and bacterivorous and fungivorous nematodes] in the rhizosphere and their trophic interactions at jointing stage of wheat. Compared with aCO₂, significant 20.2% higher shoot biomass and 26.8% total P accumulation of wheat occurred under eCO₂. The eCO₂ promoted wheat root length and AMF hyphal biomass, and increased the concentration of organic acid anions and the ALP activity, which was accompanied by significant decreases in calcium-bound inorganic P (Ca-P_i) (by 16.7%) and moderately labile organic P (by 26.5%) and an increase in available P (by 14.4%) in the rhizosphere soil. The eCO₂ also increased the growth of ALP-producing bacteria, protozoa, and bacterivorous and fungivorous nematodes in the rhizosphere, governed their diversity and community composition. In addition, the eCO₂ strengthened the trophic interactions of microbiota in rhizosphere; specifically, the eCO₂ promoted the associations between protozoa and ALP-producing bacteria, between protozoa and AMF, whereas decreased the associations between ALP-producing bacteria and nematodes. Our findings highlighted the important role of root traits and multitrophic interactions among microbiota in modulating crop P-acquisition strategies, which could advance our understanding about optimal P management in agriculture systems under global climate changes.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916408","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":"Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides","authors":"Shen Fan,&nbsp;Peng Qin,&nbsp;Jie Lu,&nbsp;Shuaitao Wang,&nbsp;Jie Zhang,&nbsp;Yan Wang,&nbsp;Aifang Cheng,&nbsp;Yan Cao,&nbsp;Wei Ding,&nbsp;Weipeng Zhang","doi":"10.1002/imt2.244","DOIUrl":"10.1002/imt2.244","url":null,"abstract":"<p>Antimicrobial peptides (AMPs) have become a viable source of novel antibiotics that are effective against human pathogenic bacteria. In this study, we construct a bank of culturable marine biofilm bacteria constituting 713 strains and their nearly complete genomes and predict AMPs using ribosome profiling and deep learning. Compared with previous approaches, ribosome profiling has improved the identification and validation of small open reading frames (sORFs) for AMP prediction. Among the 80,430 expressed sORFs, 341 are identified as candidate AMPs with high probability. Most potential AMPs have less than 40% similarity in their amino acid sequence compared to those listed in public databases. Furthermore, these AMPs are associated with bacterial groups that are not previously known to produce AMPs. Therefore, our deep learning model has acquired characteristics of unfamiliar AMPs. Chemical synthesis of 60 potential AMP sequences yields 54 compounds with antimicrobial activity, including potent inhibitory effects on various drug-resistant human pathogens. This study extends the range of AMP compounds by investigating marine biofilm microbiomes using a novel approach, accelerating AMP discovery.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 6","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11683478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916177","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":"Novel microbial modifications of bile acids and their functional implications","authors":"Dan Zheng,&nbsp;Huiheng Zhang,&nbsp;Xiaojiao Zheng,&nbsp;Aihua Zhao,&nbsp;Wei Jia","doi":"10.1002/imt2.243","DOIUrl":"https://doi.org/10.1002/imt2.243","url":null,"abstract":"<p>This review outlines the recent discoveries of bile acids that have undergone novel microbial modifications, highlighting their biological roles and the profound implications for the development of innovative therapeutic strategies. The review aims to provide valuable insights and breakthroughs for future drug candidates in the expanding field of bile acid therapeutics.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451250","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}