{"title":"Lactobacillus rhamnosus GG triggers intestinal epithelium injury in zebrafish revealing host dependent beneficial effects","authors":"Zhen Zhang, Hong-Ling Zhang, Da-Hai Yang, Qiang Hao, Hong-Wei Yang, De-Long Meng, Willem Meindert de Vos, Le-Luo Guan, Shu-Bin Liu, Tsegay Teame, Chen-Chen Gao, Chao Ran, Ya-Lin Yang, Yuan-Yuan Yao, Qian-Wen Ding, Zhi-Gang Zhou","doi":"10.1002/imt2.181","DOIUrl":"10.1002/imt2.181","url":null,"abstract":"<p><i>Lactobacillus rhamnosus</i> GG (LGG), the well-characterized human-derived probiotic strain, possesses excellent properties in the maintenance of intestinal homeostasis, immunoregulation and defense against gastrointestinal pathogens in mammals. Here, we demonstrate that the SpaC pilin of LGG causes intestinal epithelium injury by inducing cell pyroptosis and gut microbial dysbiosis in zebrafish. Dietary SpaC activates Caspase-3−GSDMEa pathways in the intestinal epithelium, promotes intestinal pyroptosis and increases lipopolysaccharide (LPS)-producing gut microbes in zebrafish. The increased LPS subsequently activates Gaspy2−GSDMEb pyroptosis pathway. Further analysis reveals the Caspase-3−GSDMEa pyroptosis is initiated by the species-specific recognition of SpaC by TLR4ba, which accounts for the species-specificity of the SpaC-inducing intestinal pyroptosis in zebrafish. The observed pyroptosis-driven gut injury and microbial dysbiosis by LGG in zebrafish suggest that host-specific beneficial/harmful mechanisms are critical safety issues when applying probiotics derived from other host species and need more attention.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140383030","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":"Arbuscular mycorrhizal fungal interactions bridge the support of root-associated microbiota for slope multifunctionality in an erosion-prone ecosystem","authors":"Tianyi Qiu, Josep Peñuelas, Yinglong Chen, Jordi Sardans, Jialuo Yu, Zhiyuan Xu, Qingliang Cui, Ji Liu, Yongxing Cui, Shuling Zhao, Jing Chen, Yunqiang Wang, Linchuan Fang","doi":"10.1002/imt2.187","DOIUrl":"10.1002/imt2.187","url":null,"abstract":"<p>The role of diverse soil microbiota in restoring erosion-induced degraded lands is well recognized. Yet, the facilitative interactions among symbiotic arbuscular mycorrhizal (AM) fungi, rhizobia, and heterotrophic bacteria, which underpin multiple functions in eroded ecosystems, remain unclear. Here, we utilized quantitative microbiota profiling and ecological network analyses to explore the interplay between the diversity and biotic associations of root-associated microbiota and multifunctionality across an eroded slope of a <i>Robinia pseudoacacia</i> plantation on the Loess Plateau. We found explicit variations in slope multifunctionality across different slope positions, associated with shifts in limiting resources, including soil phosphorus (P) and moisture. To cope with P limitation, AM fungi were recruited by <i>R. pseudoacacia</i>, assuming pivotal roles as keystones and connectors within cross-kingdom networks. Furthermore, AM fungi facilitated the assembly and composition of bacterial and rhizobial communities, collectively driving slope multifunctionality. The symbiotic association among <i>R. pseudoacacia</i>, AM fungi, and rhizobia promoted slope multifunctionality through enhanced decomposition of recalcitrant compounds, improved P mineralization potential, and optimized microbial metabolism. Overall, our findings highlight the crucial role of AM fungal-centered microbiota associated with <i>R. pseudoacacia</i> in functional delivery within eroded landscapes, providing valuable insights for the sustainable restoration of degraded ecosystems in erosion-prone regions.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140384789","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}
Ji-Hong Liu, Yizhou Zhang, Ning Zhou, Jiale He, Jing Xu, Zhao Cai, Liang Yang, Yang Liu
{"title":"Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects","authors":"Ji-Hong Liu, Yizhou Zhang, Ning Zhou, Jiale He, Jing Xu, Zhao Cai, Liang Yang, Yang Liu","doi":"10.1002/imt2.186","DOIUrl":"10.1002/imt2.186","url":null,"abstract":"<p>DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes, particularly through transcriptional regulation. With the rapid implementation of third-generation sequencing technology, we are currently experiencing a golden age of bacterial epigenomics. However, there has been a lack of comprehensive research exploring the versatility and consequential impact of bacterial DNA methylome on cellular and physiological functions. There is a critical need for a user-friendly bioinformatics tool that can effectively characterize DNA methylation modification features and predict the regulation patterns. To address this gap, the current study introduces Bacmethy, an innovative tool that utilizes SMRT-seq data and offers a range of analytical modules. First, the tool classifies methylation sites in the genome, highlighting the distinct regulations present under varying modification fractions and location enrichment. Furthermore, this tool enables us to identify regulatory region methylation and potential <i>cis</i> and <i>trans</i> interactions between methylation sites and regulatory effectors. Using benchmark data sets and our data, we show that our tool facilitates the understanding of the distinctive traits of DNA methylation modifications and predicts transcriptional regulation effects on important physiological and pathological functions. Bacmethy code is freely available, and the Docker image is downloadable. Bacmethy has been made available as a user-friendly web server interface at https://bacmethy.med.sustech.edu.cn.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.186","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140230450","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}
Tao Wang, Penghao Li, Xue Bai, Shilin Tian, Maosen Yang, Dong Leng, Hua Kui, Sujuan Zhang, Xiaomiao Yan, Qu Zheng, Pulin Luo, Changming He, Yan Jia, Zhoulin Wu, Huimin Qiu, Jing Li, Feng Wan, Muhammad A. Ali, Rurong Mao, Yong-Xin Liu, Diyan Li
{"title":"Vaginal microbiota are associated with in vitro fertilization during female infertility","authors":"Tao Wang, Penghao Li, Xue Bai, Shilin Tian, Maosen Yang, Dong Leng, Hua Kui, Sujuan Zhang, Xiaomiao Yan, Qu Zheng, Pulin Luo, Changming He, Yan Jia, Zhoulin Wu, Huimin Qiu, Jing Li, Feng Wan, Muhammad A. Ali, Rurong Mao, Yong-Xin Liu, Diyan Li","doi":"10.1002/imt2.185","DOIUrl":"10.1002/imt2.185","url":null,"abstract":"<p>The vaginal microbiome plays an essential role in the reproductive health of human females. As infertility increases worldwide, understanding the roles that the vaginal microbiome may have in infertility and in vitro fertilization (IVF) treatment outcomes is critical. To determine the vaginal microbiome composition of 1411 individuals (1255 undergoing embryo transplantation) and their associations with reproductive outcomes, clinical and biochemical features are measured, and vaginal samples are 16S rRNA sequenced. Our results suggest that both too high and too low abundance of <i>Lactobacillus</i> is not beneficial for pregnancy; a moderate abundance is more beneficial. A moderate abundance of <i>Lactobacillus crispatus</i> and <i>Lactobacillus iners</i> (~80%) (with a pregnancy rate of I-B: 54.35% and III-B: 57.73%) is found beneficial for pregnancy outcomes compared with a higher abundance (>90%) of <i>Lactobacillus</i> (I-A: 44.81% and III-A: 51.06%, respectively). The community state type (CST) IV-B (contains a high to moderate relative abundance of <i>Gardnerella vaginalis</i>) shows a similar pregnant ratio (48.09%) with I-A and III-A, and the pregnant women in this CST have a higher abundance of <i>Lactobacillus</i> species. Metagenome analysis of 71 samples shows that nonpregnant women are detected with more antibiotic-resistance genes, and Proteobacteria and Firmicutes are the main hosts. The inherent differences within and between women in different infertility groups suggest that vaginal microbes might be used to detect infertility and potentially improve IVF outcomes.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140228996","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":"Deciphering unique and shared interactions between the human gut microbiota and oral antidiabetic drugs","authors":"Huahui Ren, Zhun Shi, Fangming Yang, Shujie Wang, Fengyi Yuan, Tingting Li, Min Li, Jiahui Zhu, Junhua Li, Kui Wu, Yifei Zhang, Guang Ning, Karsten Kristiansen, Weiqing Wang, Yanyun Gu, Huanzi Zhong","doi":"10.1002/imt2.179","DOIUrl":"10.1002/imt2.179","url":null,"abstract":"<p>The administration of oral antidiabetic drugs (OADs) to patients with type 2 diabetes elicits distinct and shared changes in the gut microbiota, with acarbose and berberine exhibiting greater impacts on the gut microbiota than metformin, vildagliptin, and glipizide. The baseline gut microbiota strongly associates with treatment responses of OADs.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.179","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140245406","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}
Shi Zhong, Yu-Qing Sun, Jin-Xi Huo, Wen-Yi Xu, Ya-Nan Yang, Jun-Bo Yang, Wei-Jie Wu, Yong-Xin Liu, Chong-Ming Wu, You-Gui Li
{"title":"The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus","authors":"Shi Zhong, Yu-Qing Sun, Jin-Xi Huo, Wen-Yi Xu, Ya-Nan Yang, Jun-Bo Yang, Wei-Jie Wu, Yong-Xin Liu, Chong-Ming Wu, You-Gui Li","doi":"10.1002/imt2.180","DOIUrl":"10.1002/imt2.180","url":null,"abstract":"<p>Inflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. <i>Sanghuangporus</i> (SH), a traditional Chinese medicinal mushroom, has excellent anti-inflammatory effects and is effective at modulating the gut microbiota. Despite these attributes, the specific anticolitic effects of SH and the mechanisms through which the gut microbiota mediates its benefits remain unclear. Herein, we demonstrated that polyphenol-rich extract from SH effectively alleviated the pathological symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by modulating the gut microbiota. Treatment with SH distinctly enriched <i>Alistipes</i>, especially <i>Alistipes onderdonkii</i>, and its metabolite 5-hydroxyindole-3-acetic acid (5HIAA). Oral gavage of live <i>A. onderdonkii</i> or 5HIAA potently mitigated DSS-induced colitis in mice. Moreover, both 5HIAA and SH significantly activated the aromatic hydrocarbon receptor (AhR), and the administration of an AhR antagonist abrogated their protective effects against colitis. These results underscore the potent efficacy of SH in diminishing DSS-induced colitis through the promotion of <i>A. onderdonkii</i> and 5HIAA, ultimately activating AhR signaling. This study unveils potential avenues for developing therapeutic strategies for colitis based on the interplay between SH and the gut microbiota.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140254266","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}
Zhongji Pu, Chun-Lin Shi, Che Ok Jeon, Jingyuan Fu, Shuang-Jiang Liu, Canhui Lan, Yanlai Yao, Yong-Xin Liu, Baolei Jia
{"title":"ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum","authors":"Zhongji Pu, Chun-Lin Shi, Che Ok Jeon, Jingyuan Fu, Shuang-Jiang Liu, Canhui Lan, Yanlai Yao, Yong-Xin Liu, Baolei Jia","doi":"10.1002/imt2.178","DOIUrl":"10.1002/imt2.178","url":null,"abstract":"<p>The advent of generative artificial intelligence (AI) technologies marks a transformative moment for the scientific sphere, unlocking novel avenues to elevate scientific writing's efficiency and quality, expedite insight discovery, and enhance code development processes. Essential to leveraging these advancements is prompt engineering, a method that enhances AI interaction efficiency and quality. Despite its benefits, effective application requires blending researchers' expertise with AI, avoiding overreliance. A balanced strategy of integrating AI with independent critical thinking ensures the advancement and quality of scientific research, leveraging innovation while maintaining research integrity.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.178","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140425488","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":"Photoaffinity probe-based antimalarial target identification of artemisinin in the intraerythrocytic developmental cycle of Plasmodium falciparum","authors":"Peng Gao, Jianyou Wang, Chong Qiu, Huimin Zhang, Chen Wang, Ying Zhang, Peng Sun, Honglin Chen, Yin Kwan Wong, Jiayun Chen, Junzhe Zhang, Huan Tang, Qiaoli Shi, Yongping Zhu, Shengnan Shen, Guang Han, Chengchao Xu, Lingyun Dai, Jigang Wang","doi":"10.1002/imt2.176","DOIUrl":"https://doi.org/10.1002/imt2.176","url":null,"abstract":"<p>Malaria continues to pose a serious global health threat, and artemisinin remains the core drug for global malaria control. However, the situation of malaria resistance has become increasingly severe due to the emergence and spread of artemisinin resistance. In recent years, significant progress has been made in understanding the mechanism of action (MoA) of artemisinin. Prior research on the MoA of artemisinin mainly focused on covalently bound targets that are alkylated by artemisinin-free radicals. However, less attention has been given to the reversible noncovalent binding targets, and there is a paucity of information regarding artemisinin targets at different life cycle stages of the parasite. In this study, we identified the protein targets of artemisinin at different stages of the parasite's intraerythrocytic developmental cycle using a photoaffinity probe. Our findings demonstrate that artemisinin interacts with parasite proteins in vivo through both covalent and noncovalent modes. Extensive mechanistic studies were then conducted by integrating target validation, phenotypic studies, and untargeted metabolomics. The results suggest that protein synthesis, glycolysis, and oxidative homeostasis are critically involved in the antimalarial activities of artemisinin. In summary, this study provides fresh insights into the mechanisms underlying artemisinin's antimalarial effects and its protein targets.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.176","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140559776","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}
Chun-Hui Gao, Chengjie Chen, Turgut Akyol, Adrian Dusa, Guangchuang Yu, Bin Cao, Peng Cai
{"title":"ggVennDiagram: Intuitive Venn diagram software extended","authors":"Chun-Hui Gao, Chengjie Chen, Turgut Akyol, Adrian Dusa, Guangchuang Yu, Bin Cao, Peng Cai","doi":"10.1002/imt2.177","DOIUrl":"10.1002/imt2.177","url":null,"abstract":"<p>Highlights of ggVennDiagram include: (1) Subset/Region filling Venn diagram up to seven sets; (2) Upset plot with unlimited sets; (3) Venn Calculator for two or more sets; (4) Provide as R package, Shiny App, and TBtools plugin.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139837354","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}
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
