iMeta最新文献

{"title":"Black rice diet alleviates colorectal cancer development through modulating tryptophan metabolism and activating AHR pathway","authors":"Ling Wang,&nbsp;Yi-Xuan Tu,&nbsp;Lu Chen,&nbsp;Ke-Chun Yu,&nbsp;Hong-Kai Wang,&nbsp;Shu-Qiao Yang,&nbsp;Yuan Zhang,&nbsp;Shuai-Jie Zhang,&nbsp;Shuo Song,&nbsp;Hong-Li Xu,&nbsp;Zhu-Cheng Yin,&nbsp;Ming-Qian Feng,&nbsp;Jun-Qiu Yue,&nbsp;Xiang-Hong Huang,&nbsp;Tang Tang,&nbsp;Shao-Zhong Wei,&nbsp;Xin-Jun Liang,&nbsp;Zhen-Xia Chen","doi":"10.1002/imt2.165","DOIUrl":"10.1002/imt2.165","url":null,"abstract":"<p>Consumption of dietary fiber and anthocyanin has been linked to a lower incidence of colorectal cancer (CRC). This study scrutinizes the potential antitumorigenic attributes of a black rice diet (BRD), abundantly rich in dietary fiber and anthocyanin. Our results demonstrate notable antitumorigenic effects in mice on BRD, indicated by a reduction in both the size and number of intestinal tumors and a consequent extension in life span, compared to control diet-fed counterparts. Furthermore, fecal transplants from BRD-fed mice to germ-free mice led to a decrease in colonic cell proliferation, coupled with maintained integrity of the intestinal barrier. The BRD was associated with significant shifts in gut microbiota composition, specifically an augmentation in probiotic strains <i>Bacteroides uniformis</i> and <i>Lactobacillus</i>. Noteworthy changes in gut metabolites were also documented, including the upregulation of indole-3-lactic acid and indole. These metabolites have been identified to stimulate the intestinal aryl hydrocarbon receptor pathway, inhibiting CRC cell proliferation and colorectal tumorigenesis. In summary, these findings propose that a BRD may modulate the progression of intestinal tumors by fostering protective gut microbiota and metabolite profiles. The study accentuates the potential health advantages of whole-grain foods, emphasizing the potential utility of black rice in promoting health.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139529541","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":"PHGD: An integrative and user-friendly database for plant hormone-related genes","authors":"Shuyan Feng,&nbsp;Zhuo Liu,&nbsp;Huilong Chen,&nbsp;Nan Li,&nbsp;Tong Yu,&nbsp;Rong Zhou,&nbsp;Fulei Nie,&nbsp;Di Guo,&nbsp;Xiao Ma,&nbsp;Xiaoming Song","doi":"10.1002/imt2.164","DOIUrl":"10.1002/imt2.164","url":null,"abstract":"<p>Plant Hormone Gene Database (PHGD) database platform construction pipeline. First, we collected all reported hormone-related genes in the model plant Arabidopsis thaliana, and combined with the existing experimental background, mapped the hormone–gene interaction network to provide a blueprint. Next, we collected 469 high-quality plant genomes. Then, bioinformatics was used to identify hormone-related genes in these plants. Finally, these genetic data were programmed to be stored in a database and a platform website PHGD was built. PHGD was divided into eight modules, namely Home, Browse, Search, Resources, Download, Tools, Help, and Contact. We provided data resources and platform services to facilitate the study of plant hormones.\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":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.164","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139444907","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":"From mechanism to application: Decrypting light-regulated denitrifying microbiome through geometric deep learning","authors":"Yang Liao,&nbsp;Jing Zhao,&nbsp;Jiyong Bian,&nbsp;Ziwei Zhang,&nbsp;Siqi Xu,&nbsp;Yijian Qin,&nbsp;Shiyu Miao,&nbsp;Rui Li,&nbsp;Ruiping Liu,&nbsp;Meng Zhang,&nbsp;Wenwu Zhu,&nbsp;Huijuan Liu,&nbsp;Jiuhui Qu","doi":"10.1002/imt2.162","DOIUrl":"10.1002/imt2.162","url":null,"abstract":"<p>Regulation on denitrifying microbiomes is crucial for sustainable industrial biotechnology and ecological nitrogen cycling. The holistic genetic profiles of microbiomes can be provided by meta-omics. However, precise decryption and further applications of highly complex microbiomes and corresponding meta-omics data sets remain great challenges. Here, we combined optogenetics and geometric deep learning to form a discover–model–learn–advance (DMLA) cycle for denitrification microbiome encryption and regulation. Graph neural networks (GNNs) exhibited superior performance in integrating biological knowledge and identifying coexpression gene panels, which could be utilized to predict unknown phenotypes, elucidate molecular biology mechanisms, and advance biotechnologies. Through the DMLA cycle, we discovered the wavelength-divergent secretion system and nitrate-superoxide coregulation, realizing increasing extracellular protein production by 83.8% and facilitating nitrate removal with 99.9% enhancement. Our study showcased the potential of GNNs-empowered optogenetic approaches for regulating denitrification and accelerating the mechanistic discovery of microbiomes for in-depth research and versatile applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.162","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139380709","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":"Glucomannan promotes Bacteroides ovatus to improve intestinal barrier function and ameliorate insulin resistance","authors":"Qixing Nie,&nbsp;Yonggan Sun,&nbsp;Wenbing Hu,&nbsp;Chunhua Chen,&nbsp;Qiongni Lin,&nbsp;Shaoping Nie","doi":"10.1002/imt2.163","DOIUrl":"10.1002/imt2.163","url":null,"abstract":"<p>Bioactive dietary fiber has been proven to confer numerous health benefits against metabolic diseases based on the modification of gut microbiota. The metabolic protective effects of glucomannan have been previously reported in animal experiments and clinical trials. However, critical microbial signaling metabolites and the host targets associated with the metabolic benefits of glucomannan remain elusive. The results of this study revealed that glucomannan supplementation alleviated high-fat diet (HFD)-induced insulin resistance in mice and that its beneficial effects were dependent on the gut microbiota. Administration of glucomannan to mice promoted the growth of <i>Bacteroides ovatus</i>. Moreover, colonization with <i>B. ovatus</i> in HFD-fed mice resulted in a decrease in insulin resistance, accompanied by improved intestinal barrier integrity and reduced systemic inflammation. Furthermore, <i>B. ovatus</i>-derived indoleacetic acid (IAA) was established as a key bioactive metabolite that fortifies intestinal barrier function via activation of intestinal aryl hydrocarbon receptor (AhR), leading to an amelioration in insulin resistance. Thus, we conclude that glucomannan acts through the <i>B. ovatus</i>-IAA-intestinal AhR axis to relieve insulin resistance.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139388256","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":"Clostridium butyricum and carbohydrate active enzymes contribute to the reduced fat deposition in pigs","authors":"Lingyan Ma,&nbsp;Shiyu Tao,&nbsp;Tongxing Song,&nbsp;Wentao Lyu,&nbsp;Ying Li,&nbsp;Wen Wang,&nbsp;Qicheng Shen,&nbsp;Yan Ni,&nbsp;Jiang Zhu,&nbsp;Jiangchao Zhao,&nbsp;Hua Yang,&nbsp;Yingping Xiao","doi":"10.1002/imt2.160","DOIUrl":"10.1002/imt2.160","url":null,"abstract":"<p>Pig gastrointestinal tracts harbor a heterogeneous and dynamic ecosystem populated with trillions of microbes, enhancing the ability of the host to harvest energy from dietary carbohydrates and contributing to host adipogenesis and fatness. However, the microbial community structure and related mechanisms responsible for the differences between the fatty phenotypes and the lean phenotypes of the pigs remained to be comprehensively elucidated. Herein, we first found significant differences in microbial composition and potential functional capacity among different gut locations in Jinhua pigs with distinct fatness phenotypes. Second, we identified that Jinhua pigs with lower fatness exhibited higher levels of short-chain fatty acids in the colon, highlighting their enhanced carbohydrate fermentation capacity. Third, we explored the differences in expressed carbohydrate-active enzyme (CAZyme) in pigs, indicating their involvement in modulating fat storage. Notably, <i>Clostridium butyricum</i> might be a representative bacterial species from Jinhua pigs with lower fatness, and a significantly higher percentage of its genome was dedicated to CAZyme glycoside hydrolase family 13 (GH13). Finally, a subsequent mouse intervention study substantiated the beneficial effects of <i>C. butyricum</i> isolated from experimental pigs, suggesting that it may possess characteristics that promote the utilization of carbohydrates and hinder fat accumulation. Remarkably, when Jinhua pigs were administered <i>C. butyricum</i>, similar alterations in the gut microbiome and host fatness traits were observed, further supporting the potential role of <i>C. butyricum</i> in modulating fatness. Taken together, our findings reveal previously overlooked links between <i>C. butyricum</i> and CAZyme function, providing insight into the basic mechanisms that connect gut microbiome functions to host fatness.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.160","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139387838","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":"Soil enzyme profile analysis for indicating decomposer micro-food web","authors":"Wen Xing,&nbsp;Ning Hu,&nbsp;Zhongfang Li,&nbsp;Liangshan Feng,&nbsp;Weidong Zhang,&nbsp;Gerhard Du Preez,&nbsp;Huimin Zhang,&nbsp;Dongchu Li,&nbsp;Shunbao Lu,&nbsp;Scott X. Chang,&nbsp;Qingwen Zhang,&nbsp;Yilai Lou","doi":"10.1002/imt2.161","DOIUrl":"10.1002/imt2.161","url":null,"abstract":"<p>Highly diverse exoenzymes mediate the energy flow from substrates to the multitrophic microbiota within the soil decomposer micro-food web. Here, we used a “soil enzyme profile analysis” approach to establish a series of enzyme profile indices; those indices were hypothesized to reflect micro-food web features. We systematically evaluated the shifts in enzyme profile indices in relation to the micro-food web features in the restoration of an abandoned cropland to a natural area. We found that enzymatic C:N stoichiometry and decomposability index were significantly associated with substrate availability. Furthermore, the higher Shannon diversity index in the exoenzyme profile, especially for the C-degrading hydrolase, corresponded to a greater microbiota community diversity. The increased complexity and stability of the exoenzyme network reflected similar changes with the micro-food web networks. In addition, the gross activity of the enzyme profile as a parameter for soil multifunctionality, effectively predicted the substrate content, microbiota community size, diversity, and network complexity. Ultimately, the proposed enzymic channel index was closely associated with the traditional decomposition channel indices derived from microorganisms and nematodes. Our results showed that soil enzyme profile analysis reflected very well the decomposer food web features. Our study has important implications for projecting future climate change or anthropogenic disturbance impacts on soil decomposer micro-food web features by using soil enzyme profile analysis.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139391523","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":"Recent advances in the characterization of essential genes and development of a database of essential genes","authors":"Ya-Ting Liang,&nbsp;Hao Luo,&nbsp;Yan Lin,&nbsp;Feng Gao","doi":"10.1002/imt2.157","DOIUrl":"10.1002/imt2.157","url":null,"abstract":"<p>Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.157","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139390778","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":"Gut microbiota reshapes cancer immunotherapy efficacy: Mechanisms and therapeutic strategies","authors":"Jindong Xie,&nbsp;Manqing Liu,&nbsp;Xinpei Deng,&nbsp;Yuhui Tang,&nbsp;Shaoquan Zheng,&nbsp;Xueqi Ou,&nbsp;Hailin Tang,&nbsp;Xiaoming Xie,&nbsp;Minqing Wu,&nbsp;Yutian Zou","doi":"10.1002/imt2.156","DOIUrl":"10.1002/imt2.156","url":null,"abstract":"<p>Gut microbiota is essential for maintaining local and systemic immune homeostasis in the presence of bacterial challenges. It has been demonstrated that microbiota play contrasting roles in cancer development as well as anticancer immunity. Cancer immunotherapy, a novel anticancer therapy that relies on the stimulation of host immunity, has suffered from a low responding rate and incidence of severe immune-related adverse events (irAEs). Previous studies have demonstrated that the diversity and composition of gut microbiota were associated with the heterogeneity of therapeutic effects. Therefore, alteration in microbiota taxa can lead to improved clinical outcomes in immunotherapy. In this review, we determine whether microbiota composition or microbiota-derived metabolites are linked to responses to immunotherapy and irAEs. Moreover, we discuss various approaches to improve immunotherapy efficacy or reduce toxicities by modulating microbiota composition.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.156","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139128119","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":"Promising dawn in the management of pulmonary hypertension: The mystery veil of gut microbiota","authors":"Yicheng Yang,&nbsp;Hanwen Zhang,&nbsp;Yaoyao Wang,&nbsp;Jing Xu,&nbsp;Songren Shu,&nbsp;Peizhi Wang,&nbsp;Shusi Ding,&nbsp;Yuan Huang,&nbsp;Lemin Zheng,&nbsp;Yuejin Yang,&nbsp;Changming Xiong","doi":"10.1002/imt2.159","DOIUrl":"10.1002/imt2.159","url":null,"abstract":"<p>The gut microbiota is a complex community of microorganisms inhabiting the intestinal tract, which plays a vital role in human health. It is intricately involved in the metabolism, and it also affects diverse physiological processes. The gut–lung axis is a bidirectional pathway between the gastrointestinal tract and the lungs. Recent research has shown that the gut microbiome plays a crucial role in immune response regulation in the lungs and the development of lung diseases. In this review, we present the interrelated factors concerning gut microbiota and the associated metabolites in pulmonary hypertension (PH), a lethal disease characterized by elevated pulmonary vascular pressure and resistance. Our research team explored the role of gut-microbiota-derived metabolites in cardiovascular diseases and established the correlation between metabolites such as putrescine, succinate, trimethylamine N-oxide (TMAO), and N, N, N-trimethyl-5-aminovaleric acid with the diseases. Furthermore, we found that specific metabolites, such as TMAO and betaine, have significant clinical value in PH, suggesting their potential as biomarkers in disease management. In detailing the interplay between the gut microbiota, their metabolites, and PH, we underscored the potential therapeutic approaches modulating this microbiota. Ultimately, we endeavor to alleviate the substantial socioeconomic burden associated with this disease. This review presents a unique exploratory analysis of the link between gut microbiota and PH, intending to propel further investigations in the gut–lung axis.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139128543","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":"Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome","authors":"Dong-Rui Chen,&nbsp;Ke Cheng,&nbsp;Lei Wan,&nbsp;Chao-Yue Cui,&nbsp;Gong Li,&nbsp;Dong-Hao Zhao,&nbsp;Yang Yu,&nbsp;Xiao-Ping Liao,&nbsp;Ya-Hong Liu,&nbsp;Alaric W. D'Souza,&nbsp;Xin-Lei Lian,&nbsp;Jian Sun","doi":"10.1002/imt2.158","DOIUrl":"10.1002/imt2.158","url":null,"abstract":"<p>Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.158","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139126164","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}