Jing Li, Si-Yuan Wang, Kai-Xin Yan, Pan Wang, Jie Jiao, Yi-Dan Wang, Mu-Lei Chen, Ying Dong, Jiu-Chang Zhong
{"title":"Intestinal microbiota by angiotensin receptor blocker therapy exerts protective effects against hypertensive damages","authors":"Jing Li, Si-Yuan Wang, Kai-Xin Yan, Pan Wang, Jie Jiao, Yi-Dan Wang, Mu-Lei Chen, Ying Dong, Jiu-Chang Zhong","doi":"10.1002/imt2.222","DOIUrl":"10.1002/imt2.222","url":null,"abstract":"<p>Dysbiosis of the gut microbiota has been implicated in hypertension, and drug–host–microbiome interactions have drawn considerable attention. However, the influence of angiotensin receptor blocker (ARB)-shaped gut microbiota on the host is not fully understood. In this work, we assessed the alterations of blood pressure (BP), vasculatures, and intestines following ARB-modified gut microbiome treatment and evaluated the changes in the intestinal transcriptome and serum metabolome in hypertensive rats. Hypertensive patients with well-controlled BP under ARB therapy were recruited as human donors, spontaneously hypertensive rats (SHRs) receiving normal saline or valsartan were considered animal donors, and SHRs were regarded as recipients. Histological and immunofluorescence staining was used to assess the aorta and small intestine, and 16S rRNA amplicon sequencing was performed to examine gut bacteria. Transcriptome and metabonomic analyses were conducted to determine the intestinal transcriptome and serum metabolome, respectively. Notably, ARB-modified fecal microbiota transplantation (FMT), results in marked decreases in systolic BP levels, collagen deposition and reactive oxygen species accumulation in the vasculature, and alleviated intestinal structure impairments in SHRs. These changes were linked with the reconstruction of the gut microbiota in SHR recipients post-FMT, especially with a decreased abundance of <i>Lactobacillus</i>, <i>Aggregatibacter</i>, and <i>Desulfovibrio</i>. Moreover, ARB-treated microbes contributed to increased intestinal <i>Ciart</i>, <i>Per1</i>, <i>Per2</i>, <i>Per3</i>, and <i>Cipc</i> gene levels and decreased <i>Nfil3</i> and <i>Arntl</i> expression were detected in response to ARB-treated microbes. More importantly, circulating metabolites were dramatically reduced in ARB-FMT rats, including 6beta-Hydroxytestosterone and Thromboxane B2. In conclusion, ARB-modified gut microbiota exerts protective roles in vascular remodeling and injury, metabolic abnormality and intestinal dysfunctions, suggesting a pivotal role in mitigating hypertension and providing insights into the cross-talk between antihypertensive medicines and the gut microbiome.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.222","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141825005","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 functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits","authors":"Ming-Yuan Xue, Yun-Yi Xie, Xin-Wei Zang, Yi-Fan Zhong, Xiao-Jiao Ma, Hui-Zeng Sun, Jian-Xin Liu","doi":"10.1002/imt2.225","DOIUrl":"10.1002/imt2.225","url":null,"abstract":"<p>Over the years, microbiome research has achieved tremendous advancements driven by culture-independent meta-omics approaches. Despite extensive research, our understanding of the functional roles and causal effects of the microbiome on phenotypes remains limited. In this study, we focused on the rumen metaproteome, combining it with metatranscriptome and metabolome data to accurately identify the active functional distributions of rumen microorganisms and specific functional groups that influence feed efficiency. By integrating host genetics data, we established the potentially causal relationships between microbes-proteins/metabolites-phenotype, and identified specific patterns in which functional groups of rumen microorganisms influence host feed efficiency. We found a causal link between <i>Selenomonas bovis</i> and rumen carbohydrate metabolism, potentially mediated by bacterial chemotaxis and a two-component regulatory system, impacting feed utilization efficiency of dairy cows. Our study on the nutrient utilization functional groups in the rumen of high-feed-efficiency dairy cows, along with the identification of key microbiota functional proteins and their potentially causal relationships, will help move from correlation to causation in rumen microbiome research. This will ultimately enable precise regulation of the rumen microbiota for optimized ruminant production.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141647117","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}
Dacheng Wang, Yingqiao Wan, Dekun Liu, Ning Wang, Jingni Wu, Qin Gu, Huijun Wu, Xuewen Gao, Yiming Wang
{"title":"Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases","authors":"Dacheng Wang, Yingqiao Wan, Dekun Liu, Ning Wang, Jingni Wu, Qin Gu, Huijun Wu, Xuewen Gao, Yiming Wang","doi":"10.1002/imt2.223","DOIUrl":"10.1002/imt2.223","url":null,"abstract":"<p>Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.223","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141833129","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":"Probio-M9, a breast milk-originated probiotic, alleviates mastitis and enhances antibiotic efficacy: Insights into the gut–mammary axis","authors":"Jie Yu, Weicheng Li, Ruibo Xu, Xiaoye Liu, Guangqi Gao, Lai-Yu Kwok, Yongfu Chen, Zhihong Sun, Wenjun Liu, Heping Zhang","doi":"10.1002/imt2.224","DOIUrl":"10.1002/imt2.224","url":null,"abstract":"<p>Breast milk naturally contains lactic acid bacteria, but their precise origin remains a subject of debate. In this study, we utilized a rat mastitis animal model to investigate the potential of a breast milk-derived probiotic strain, <i>Lacticaseibacillus rhamnosus</i> Probio-M9, in alleviating mastitis and enhancing the efficacy of antibiotic treatment. Through histopathological analysis of mammary tissue, we observed that Probio-M9 effectively relieved mastitis, mitigated inflammation, and improved the response to antibiotic treatment. Metagenomic analysis further revealed that Probio-M9 enhanced interactions among gut microbes, accompanied by an increase in the relative abundance of <i>Ruminococcaceae</i> and the regulation of specific genes and carbohydrate-active enzymes, subsequently impacting host immunity. Additionally, an intriguing finding was the translocation of live Probio-M9 from the gut to the mammary tissue only during bacterial mastitis and lactation, likely facilitated through lymphatic circulation. These findings advance our understanding of the intricate gut–mammary axis and provide valuable insights into the potential health benefits of probiotic interventions.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141664228","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}
Jun Wang, Qian Li, Yuanwang Qiu, Simo Kitanovski, Chen Wang, Chenxia Zhang, Fahong Li, Xiaoguang Li, Zhenfeng Zhang, Lihua Huang, Jiming Zhang, Daniel Hoffmann, Mengji Lu, Hongzhou Lu
{"title":"Cell-type-specific expression analysis of liver transcriptomics with clinical parameters to decipher the cause of intrahepatic inflammation in chronic hepatitis B","authors":"Jun Wang, Qian Li, Yuanwang Qiu, Simo Kitanovski, Chen Wang, Chenxia Zhang, Fahong Li, Xiaoguang Li, Zhenfeng Zhang, Lihua Huang, Jiming Zhang, Daniel Hoffmann, Mengji Lu, Hongzhou Lu","doi":"10.1002/imt2.221","DOIUrl":"10.1002/imt2.221","url":null,"abstract":"<p>Functional cure for chronic hepatitis B (CHB) remains challenging due to the lack of direct intervention methods for hepatic inflammation. Multi-omics research offers a promising approach to understand hepatic inflammation mechanisms in CHB. A Bayesian linear model linked gene expression with clinical parameters, and population-specific expression analysis (PSEA) refined bulk gene expression into specific cell types across different clinical phases. These models were integrated into our analysis of key factors like inflammatory cells, immune activation, T cell exhaustion, chemokines, receptors, and interferon-stimulated genes (ISGs). Validation through multi-immune staining in liver specimens from CHB patients bolstered our findings. In CHB patients, increased gene expression related to immune cell activation and migration was noted. Marker genes of macrophages, T cells, immune-negative regulators, chemokines, and ISGs showed a positive correlation with serum alanine aminotransferase (ALT) levels but not hepatitis B virus DNA levels. The PSEA model confirmed T cells as the source of exhausted regulators, while macrophages primarily contributed to chemokine expression. Upregulated ISGs (<i>ISG20, IFI16, TAP2, GBP1, PSMB9</i>) in the hepatitis phase were associated with T cell and macrophage infiltration and positively correlated with ALT levels. Conversely, another set of ISGs (<i>IFI44, ISG15, IFI44L, IFI6, MX1</i>) mainly expressed by hepatocytes and B cells showed no correlation with ALT levels. Our study presents a multi-omics analysis integrating bulk transcriptomic, single-cell sequencing data, and clinical data from CHB patients to decipher the cause of intrahepatic inflammation in CHB. The findings confirm that macrophages secrete chemokines like CCL20, recruiting exhausted T cells into liver tissue; concurrently, hepatocyte innate immunity is suppressed, hindering the antiviral effects of ISGs.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141677555","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}
Hao Zhang, Jiawan Wang, Jianghua Shen, Siqi Chen, Hailong Yuan, Xuan Zhang, Xu Liu, Ying Yu, Xinran Li, Zeyu Gao, Yaohui Wang, Jun Wang, Moshi Song
{"title":"Prophylactic supplementation with Bifidobacterium infantis or its metabolite inosine attenuates cardiac ischemia/reperfusion injury","authors":"Hao Zhang, Jiawan Wang, Jianghua Shen, Siqi Chen, Hailong Yuan, Xuan Zhang, Xu Liu, Ying Yu, Xinran Li, Zeyu Gao, Yaohui Wang, Jun Wang, Moshi Song","doi":"10.1002/imt2.220","DOIUrl":"10.1002/imt2.220","url":null,"abstract":"<p>Emerging evidence has demonstrated the profound impact of the gut microbiome on cardiovascular diseases through the production of diverse metabolites. Using an animal model of myocardial ischemia–reperfusion (I/R) injury, we found that the prophylactic administration of a well-known probiotic, <i>Bifidobacterium infantis</i> (<i>B. infantis</i>), exhibited cardioprotective effects in terms of preserving cardiac contractile function and preventing adverse cardiac remodeling following I/R and that these cardioprotective effects were recapitulated by its metabolite inosine. Transcriptomic analysis further revealed that inosine mitigated I/R-induced cardiac inflammation and cell death. Mechanistic investigations elucidated that inosine suppressed the production of pro-inflammatory cytokines and reduced the numbers of dendritic cells and natural killer cells, achieved through the activation of the adenosine A2A receptor (A2AR) that when inhibited abrogated the cardioprotective effects of inosine. Additionally, in vitro studies using C2C12 myoblasts revealed that inosine attenuated cell death by serving as an alternative carbon source for adenosine triphosphate (ATP) generation through the purine salvage pathway when subjected to oxygen-glucose deprivation/reoxygenation that simulated myocardial I/R injury. Likewise, inosine reversed the I/R-induced decrease in ATP levels in mouse hearts. Taken together, our findings indicate that <i>B. infantis</i> or its metabolite inosine exerts cardioprotective effects against I/R by suppressing cardiac inflammation and attenuating cardiac cell death, suggesting prophylactic therapeutic options for acute ischemic cardiac injury.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141685597","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":"MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility","authors":"Xin Wei, Li Guo, Hongliu Cai, Silan Gu, Lingling Tang, Yuxin Leng, Minghui Cheng, Guojun He, Yijiao Han, Xindie Ren, Baoyue Lin, Longxian Lv, Huanzhang Shao, Mingqiang Wang, Hongyu Wang, Dan Dang, Shengfeng Wang, Nan Wang, Peng Shen, Qianqian Wang, Yinghe Xu, Yongpo Jiang, Ning Zhang, Xuwei He, Xuntao Deng, Muhua Dai, Lin Zhong, Yonghui Xiong, Yujie Pan, Kankai Tang, Fengqi Liu, Bin Yang, Lili Ren, Jianwei Wang, Chao Jiang, Lingtong Huang","doi":"10.1002/imt2.218","DOIUrl":"https://doi.org/10.1002/imt2.218","url":null,"abstract":"<p>The MASS cohort comprises 2000 ICU patients with severe pneumonia, covering community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, sourced from 19 hospitals across 10 cities in three provinces. A wide array of samples including bronchoalveolar lavage fluid, sputum, feces, and whole blood are longitudinally collected throughout patients' ICU stays. The cohort study seeks to uncover the dynamics of lung and gut microbiomes and their associations with severe pneumonia and host susceptibility, integrating deep metagenomics and transcriptomics with detailed clinical data.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.218","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967097","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":"Majorbio Cloud 2024: Update single-cell and multiomics workflows","authors":"Chang Han, Caiping Shi, Linmeng Liu, Jichen Han, Qianqian Yang, Yan Wang, Xiaodan Li, Wenyao Fu, Hao Gao, Huasheng Huang, Xianglin Zhang, Kegang Yu","doi":"10.1002/imt2.217","DOIUrl":"https://doi.org/10.1002/imt2.217","url":null,"abstract":"<p>Majorbio Cloud (https://cloud.majorbio.com/) is a one-stop online analytic platform aiming at promoting the development of bioinformatics services, narrowing the gap between wet and dry experiments, and accelerating the discoveries for the life sciences community. In 2024, three single-omics workflows, two multiomics workflows, and extensions were newly released to facilitate omics data mining and interpretation.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.217","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967098","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":"Smaller microorganisms outcompete larger ones in resistance and functional effects under disturbed agricultural ecosystems","authors":"Chunling Liang, Jiejun Qi, Wenyuan Wu, Xingyu Chen, Mingyu Li, Yu Liu, Ziheng Peng, Shi Chen, Haibo Pan, Beibei Chen, Jiai Liu, Yihe Wang, Sanfeng Chen, Sen Du, Gehong Wei, Shuo Jiao","doi":"10.1002/imt2.219","DOIUrl":"https://doi.org/10.1002/imt2.219","url":null,"abstract":"<p>Body size is a key ecological trait of soil microorganisms related to their adaptation to environmental changes. In this study, we reveal that the smaller microorganisms show stronger community resistance than larger organisms in both maize and rice soil. Compared with larger organisms, smaller microorganisms have higher diversity and broader niche breadth to deploy survival strategies, because of which they are less affected by environmental selection and thus survive in complex and various kinds of environments. In addition, the strong correlation between smaller microorganisms and ecosystem functions reflects their greater metabolic flexibility and illustrates their significant roles in adaptation to continuously changing environments. This research highlights the importance of body size in maintaining stability of the soil microbiome and forecasting agroecosystem dynamics under environmental disturbances.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968086","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":"Genetic manipulations of nonmodel gut microbes","authors":"Wen-Bing Jin, Chun-Jun Guo","doi":"10.1002/imt2.216","DOIUrl":"https://doi.org/10.1002/imt2.216","url":null,"abstract":"<p>Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The “bottleneck” preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step-by-step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram-negative <i>Bacteroidia</i> and Gram-positive <i>Clostridia</i> organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.216","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968084","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}