Qixing Nie, Yonggan Sun, Wenbing Hu, Chunhua Chen, Qiongni Lin, Shaoping Nie
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 Bacteroides ovatus. Moreover, colonization with B. ovatus in HFD-fed mice resulted in a decrease in insulin resistance, accompanied by improved intestinal barrier integrity and reduced systemic inflammation. Furthermore, B. ovatus-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 B. ovatus-IAA-intestinal AhR axis to relieve insulin resistance.
{"title":"Glucomannan promotes Bacteroides ovatus to improve intestinal barrier function and ameliorate insulin resistance","authors":"Qixing Nie, Yonggan Sun, Wenbing Hu, Chunhua Chen, Qiongni Lin, 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":null,"pages":null},"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}
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, Clostridium butyricum 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 C. butyricum 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 C. butyricum, similar alterations in the gut microbiome and host fatness traits were observed, further supporting the potential role of C. butyricum in modulating fatness. Taken together, our findings reveal previously overlooked links between C. butyricum and CAZyme function, providing insight into the basic mechanisms that connect gut microbiome functions to host fatness.
{"title":"Clostridium butyricum and carbohydrate active enzymes contribute to the reduced fat deposition in pigs","authors":"Lingyan Ma, Shiyu Tao, Tongxing Song, Wentao Lyu, Ying Li, Wen Wang, Qicheng Shen, Yan Ni, Jiang Zhu, Jiangchao Zhao, Hua Yang, 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":null,"pages":null},"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}
Wen Xing, Ning Hu, Zhongfang Li, Liangshan Feng, Weidong Zhang, Gerhard Du Preez, Huimin Zhang, Dongchu Li, Shunbao Lu, Scott X. Chang, Qingwen Zhang, Yilai Lou
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.
在土壤分解者微食物网中,高度多样化的外酶介导着从基质到多营养微生物群的能量流。在这里,我们使用 "土壤酶谱分析 "方法建立了一系列酶谱指数,并假设这些指数能反映微食物网的特征。在将废弃耕地恢复为自然区域的过程中,我们系统地评估了与微食物网特征相关的酶剖面指数的变化。我们发现,酶的 C:N 配比和可分解指数与基质的可用性有明显的关联。此外,外切酶(尤其是 C 降解水解酶)的香农多样性指数越高,微生物群落的多样性就越大。外切酶网络复杂性和稳定性的增加反映了微食物网网络的类似变化。此外,作为土壤多功能性的参数,酶的总活性能有效预测底物含量、微生物群落规模、多样性和网络复杂性。最终,所提出的酶通道指数与传统的微生物和线虫分解通道指数密切相关。我们的研究结果表明,土壤酶谱分析很好地反映了分解者食物网的特征。我们的研究对于利用土壤酶剖面分析预测未来气候变化或人为干扰对土壤分解者微食物网特征的影响具有重要意义。
{"title":"Soil enzyme profile analysis for indicating decomposer micro-food web","authors":"Wen Xing, Ning Hu, Zhongfang Li, Liangshan Feng, Weidong Zhang, Gerhard Du Preez, Huimin Zhang, Dongchu Li, Shunbao Lu, Scott X. Chang, Qingwen Zhang, 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":null,"pages":null},"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}
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.
{"title":"Recent advances in the characterization of essential genes and development of a database of essential genes","authors":"Ya-Ting Liang, Hao Luo, Yan Lin, 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":null,"pages":null},"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}
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.
{"title":"Gut microbiota reshapes cancer immunotherapy efficacy: Mechanisms and therapeutic strategies","authors":"Jindong Xie, Manqing Liu, Xinpei Deng, Yuhui Tang, Shaoquan Zheng, Xueqi Ou, Hailin Tang, Xiaoming Xie, Minqing Wu, 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":null,"pages":null},"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}
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.
{"title":"Promising dawn in the management of pulmonary hypertension: The mystery veil of gut microbiota","authors":"Yicheng Yang, Hanwen Zhang, Yaoyao Wang, Jing Xu, Songren Shu, Peizhi Wang, Shusi Ding, Yuan Huang, Lemin Zheng, Yuejin Yang, 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":null,"pages":null},"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}
Dong-Rui Chen, Ke Cheng, Lei Wan, Chao-Yue Cui, Gong Li, Dong-Hao Zhao, Yang Yu, Xiao-Ping Liao, Ya-Hong Liu, Alaric W. D'Souza, Xin-Lei Lian, Jian Sun
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.
{"title":"Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome","authors":"Dong-Rui Chen, Ke Cheng, Lei Wan, Chao-Yue Cui, Gong Li, Dong-Hao Zhao, Yang Yu, Xiao-Ping Liao, Ya-Hong Liu, Alaric W. D'Souza, Xin-Lei Lian, 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":null,"pages":null},"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}
Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene IGF2BP1 associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in MITF intron, which triggers a novel transcript of MITF, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.
结构变异(SV)是驯化和改良性状的主要来源。我们展示了利用五个基因组组装构建的首个鸭泛基因组,共获取了 40.98 Mb 的新序列。该泛基因组连同高深度测序数据(∼46.5×)共鉴定出101,041个SV,其中很大一部分来自转座元件(TE)活动。许多源自基因体或调控区的转座元件 SV 与鸭的驯化和改良有关。通过将定量遗传学与分子实验相结合,我们首次发现了一个 6945 bp 的吉普赛插入基因,它是与鸭体重相关的主要基因 IGF2BP1 的功能突变。据我们所知,这个吉普赛插入基因是禽类中对体重影响最大的基因(占表型变异的 27.61%)。此外,我们还研究了 MITF 内含子中另一个 6634 bp 的吉普赛插入片段,它触发了 MITF 的一个新转录本,从而促进了白羽的形成。我们的研究结果凸显了在基因组学研究中使用泛基因组作为参考的重要性,并阐明了转座子在性状形成和家畜育种中的影响。
{"title":"Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution","authors":"Kejun Wang, Guoying Hua, Jingyi Li, Yu Yang, Chenxi Zhang, Lan Yang, Xiaoyu Hu, Armin Scheben, Yanan Wu, Ping Gong, Shuangjie Zhang, Yanfeng Fan, Tao Zeng, Lizhi Lu, Yanzhang Gong, Ruirui Jiang, Guirong Sun, Yadong Tian, Xiangtao Kang, Haifei Hu, Wenting Li","doi":"10.1002/imt2.154","DOIUrl":"10.1002/imt2.154","url":null,"abstract":"<p>Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ∼40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (∼46.5×) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchoring in a gene body or regulatory region are linked to duck's domestication and improvement. By combining quantitative genetics with molecular experiments, we, for the first time, unraveled a 6945 bp Gypsy insertion as a functional mutation of the major gene <i>IGF2BP1</i> associated with duck bodyweight. This Gypsy insertion, to our knowledge, explains the largest effect on bodyweight among avian species (27.61% of phenotypic variation). In addition, we also examined another 6634 bp Gypsy insertion in <i>MITF</i> intron, which triggers a novel transcript of <i>MITF</i>, thereby contributing to the development of white plumage. Our findings highlight the importance of using a pan-genome as a reference in genomics studies and illuminate the impact of transposons in trait formation and livestock breeding.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138966064","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}
Xueli Zhang, Min Li, Siting Ye, Ke Shen, Haining Yuan, Shoaib Bakhtyar, Qiliang Peng, Yongsheng Liu, Yingying Wang, Manshi Li, Chi Zhang, Yixin Wang, Xiaohe Bai, Shunming Liu, Ke Zhao, Bairong Shen, Dirk Repsilber, Guang Hu, Hong Zhang, Xiao-Feng Sun
The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed CBD2, which includes information on 1569 newly reported biomarkers derived from different biological sources (DNA, RNA, protein, and others) and clinical applications (diagnosis, treatment, and prognosis). CBD2 also incorporates information on nonbiomarkers that have been identified as unsuitable for use as biomarkers in CRC. A key new feature of CBD2 is its network analysis function, by which users can investigate the visible and topological network between biomarkers and identify their relevant pathways. CBD2 also allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multidrug, multitarget, multipathway analyses, toward facilitating the design of polypharmacological treatments for CRC. CBD2 is freely available at http://www.eyeseeworld.com/cbd.
结直肠癌(CRC)生物标志物的快速发展需要一个整合的、更新的存储库。为此,我们构建了结直肠癌生物标志物数据库(Colorectal Cancer Biomarker Database, CBD),收集并展示了前期研究中筛选出的870个结直肠癌生物标志物的生物医学信息。在CBD的基础上,我们现在开发了CBD2,其中包括1569个新报道的生物标志物的信息,这些生物标志物来自不同的生物来源(DNA、RNA、蛋白质等)和临床应用(诊断、治疗和预后)。CBD2还纳入了已确定不适合作为结直肠癌生物标志物的非生物标志物的信息。CBD2的一个关键新功能是其网络分析功能,通过该功能,用户可以研究生物标志物之间的可见和拓扑网络,并确定其相关途径。CBD2还允许用户查询一系列化学物质、药物组合或多个靶点,以实现多药物、多靶点、多途径分析,促进CRC多药物治疗的设计。CBD2可在http://www.eyeseeworld.com/cbd免费获得。
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The CHINAGUT Conference, a biennial event dedicated to gut science, has grown significantly since its inception in 2018. Its 4th iteration, CHINAGUT 2023, was held from May 19 to 22 at the Beijing National Convention Center, attracting over 10,000 attendees. This large-scale academic interchange, organized by numerous academic and industrial entities, has become China's premier conference on gut-related research.
This year's conference showcased an evolved content structure with a comprehensive call for submissions, channeling over 60% of oral presentations from submitted abstracts. The conference was organized into 14 major academic tracks reflecting hot research fields, including Microbiome, Translational Medicine, Nutrition and Food, Animal Gut, Immunology, Metabolism, Neurology, Gut Physiology and Development, Oncology, Inflammatory Bowel Disease (IBD), Holistic Integrated Enterology, Special Populations, Technology and Methods, and One Health, with two additional augment tracks on Career Development and Public Science Education. The event hosted 35 academic sessions, drawing over 300 global scholars contributing to over 400 presentations and exhibiting about 1000 posters.
This conference report navigates through the highlights of the conference, chiefly focusing on plenary presentations, salient points from concurrent sessions, and the accolade of awards.
The opening ceremony highlighted seven keynote presentations, unveiling a rich tapestry of advancements in gut science research and industry. Covering a broad spectrum from gastrointestinal cancer, metabolic diseases, and intestinal immunity to the gut–lung axis, microbial interventions, cohort studies, and nutritional epidemiology, these talks collectively spotlight the interdisciplinary evolution of gut science, showcasing innovative pathways for solutions and therapies.
CHINAGUT has once again shone the spotlight on remarkable individuals and burgeoning talents in the field of gut health research and industry. The accolades were bestowed in three major categories, highlighting the remarkable work of both seasoned and emerging researchers and industry professionals.
The much-anticipated R Awards, organized by the R Institute, were segmented into two categories: “Scientist of the Year” and “Gut Industry Person of the Year.” This year's distinguished “Scientist of the Year” award was shared by Prof. Changtao Jiang from Peking University for his groundbreaking work on gut microbiota and metabolic diseases, Prof. Faming Zhang from Nanjing Medical University for his clinical research in microbiota transplantation, particularly the development of WMT technique, and Prof. Wei Chen from Jiangnan University for his enduring commitment over two decades toward developing probiotics native to China, establishing the nation's largest proprietary probiotic strain bank. The “Gut Industry Person of the Year” was awarded to industry trailblazers—Mr. Guoxun Xiao, the founde
{"title":"Conference report: CHINAGUT 2023","authors":"Danyi Li, CHINAGUT 2023 Organizing Committee","doi":"10.1002/imt2.153","DOIUrl":"https://doi.org/10.1002/imt2.153","url":null,"abstract":"<p>The CHINAGUT Conference, a biennial event dedicated to gut science, has grown significantly since its inception in 2018. Its 4th iteration, CHINAGUT 2023, was held from May 19 to 22 at the Beijing National Convention Center, attracting over 10,000 attendees. This large-scale academic interchange, organized by numerous academic and industrial entities, has become China's premier conference on gut-related research.</p><p>This year's conference showcased an evolved content structure with a comprehensive call for submissions, channeling over 60% of oral presentations from submitted abstracts. The conference was organized into 14 major academic tracks reflecting hot research fields, including Microbiome, Translational Medicine, Nutrition and Food, Animal Gut, Immunology, Metabolism, Neurology, Gut Physiology and Development, Oncology, Inflammatory Bowel Disease (IBD), Holistic Integrated Enterology, Special Populations, Technology and Methods, and One Health, with two additional augment tracks on Career Development and Public Science Education. The event hosted 35 academic sessions, drawing over 300 global scholars contributing to over 400 presentations and exhibiting about 1000 posters.</p><p>This conference report navigates through the highlights of the conference, chiefly focusing on plenary presentations, salient points from concurrent sessions, and the accolade of awards.</p><p>The opening ceremony highlighted seven keynote presentations, unveiling a rich tapestry of advancements in gut science research and industry. Covering a broad spectrum from gastrointestinal cancer, metabolic diseases, and intestinal immunity to the gut–lung axis, microbial interventions, cohort studies, and nutritional epidemiology, these talks collectively spotlight the interdisciplinary evolution of gut science, showcasing innovative pathways for solutions and therapies.</p><p>CHINAGUT has once again shone the spotlight on remarkable individuals and burgeoning talents in the field of gut health research and industry. The accolades were bestowed in three major categories, highlighting the remarkable work of both seasoned and emerging researchers and industry professionals.</p><p>The much-anticipated R Awards, organized by the R Institute, were segmented into two categories: “Scientist of the Year” and “Gut Industry Person of the Year.” This year's distinguished “Scientist of the Year” award was shared by Prof. Changtao Jiang from Peking University for his groundbreaking work on gut microbiota and metabolic diseases, Prof. Faming Zhang from Nanjing Medical University for his clinical research in microbiota transplantation, particularly the development of WMT technique, and Prof. Wei Chen from Jiangnan University for his enduring commitment over two decades toward developing probiotics native to China, establishing the nation's largest proprietary probiotic strain bank. The “Gut Industry Person of the Year” was awarded to industry trailblazers—Mr. Guoxun Xiao, the founde","PeriodicalId":73342,"journal":{"name":"iMeta","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.153","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138468638","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}