Engineering Microbiology最新文献_第4页

Altered interaction network in the gut microbiota of current cigarette smokers 当前吸烟者肠道微生物群相互作用网络的改变

Engineering Microbiology Pub Date : 2024-01-18 DOI: 10.1016/j.engmic.2024.100138

Zhouhai Zhu , Meng Wang , Ying Guan , Meng Li , Qiyuan Peng , Ning Zheng , Wenbin Ma

{"title":"Altered interaction network in the gut microbiota of current cigarette smokers","authors":"Zhouhai Zhu , Meng Wang , Ying Guan , Meng Li , Qiyuan Peng , Ning Zheng , Wenbin Ma","doi":"10.1016/j.engmic.2024.100138","DOIUrl":"10.1016/j.engmic.2024.100138","url":null,"abstract":"<div><p>The association between cigarette smoking and the gut microbiota remains unclear, and there is no agreement on how smoking affects the composition of gut microorganisms. In this study, the relationship between smoking status and gut microbial composition was investigated by performing 16S rRNA gene amplicon sequencing analysis of stool samples from 80 healthy Chinese adults. The results showed that smoking did not cause significant changes to the composition and microbial functional pathways of the gut microbiota. However, smoking altered the relative abundance of several specific taxa, where <em>Phascolarctobacterium</em> and <em>Fusobacterium</em> increased and <em>Dialister</em> decreased. Notably, our analysis revealed that smoking introduced more microbial interactions to the interaction network and decreased its modularity. Overall, this study provides new insights into the association between smoking status and the gut microbiota.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 2","pages":"Article 100138"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370324000018/pdfft?md5=8daccfb83c08c8c63fcdd652a9093808&pid=1-s2.0-S2667370324000018-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139637241","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}

引用次数: 0

Heterologous expression facilitates the discovery and characterization of marine microbial natural products 异源表达有助于发现和鉴定海洋微生物天然产物

Engineering Microbiology Pub Date : 2023-12-19 DOI: 10.1016/j.engmic.2023.100137

Shuang Zhao , Ruiying Feng , Yuan Gu , Liyuan Han , Xiaomei Cong , Yang Liu , Shuo Liu , Qiyao Shen , Liujie Huo , Fu Yan

{"title":"Heterologous expression facilitates the discovery and characterization of marine microbial natural products","authors":"Shuang Zhao , Ruiying Feng , Yuan Gu , Liyuan Han , Xiaomei Cong , Yang Liu , Shuo Liu , Qiyao Shen , Liujie Huo , Fu Yan","doi":"10.1016/j.engmic.2023.100137","DOIUrl":"10.1016/j.engmic.2023.100137","url":null,"abstract":"<div><p>Microbial natural products and their derivatives have been developed as a considerable part of clinical drugs and agricultural chemicals. Marine microbial natural products exhibit diverse chemical structures and bioactivities with substantial potential for the development of novel pharmaceuticals. However, discovering compounds with new skeletons from marine microbes remains challenging. In recent decades, multiple approaches have been developed to discover novel marine microbial natural products, among which heterologous expression has proven to be an effective method. Facilitated by large DNA cloning and comparative metabolomic technologies, a few novel bioactive natural products from marine microorganisms have been identified by the expression of their biosynthetic gene clusters (BGCs) in heterologous hosts. Heterologous expression is advantageous for characterizing gene functions and elucidating the biosynthetic mechanisms of natural products. This review provides an overview of recent progress in heterologous expression-guided discovery, biosynthetic mechanism elucidation, and yield optimization of natural products from marine microorganisms and discusses the future directions of the heterologous expression strategy in facilitating novel natural product exploitation.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 2","pages":"Article 100137"},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000693/pdfft?md5=327efcf30168d96356c4e7af90784416&pid=1-s2.0-S2667370323000693-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138991756","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}

引用次数: 0

Chromatographic and Mass Spectroscopic Guided Discovery of Trichoderma Peptaibiotics and their Bioactivity 色谱和质谱引导下的毛霉多肽及其生物活性的发现

Engineering Microbiology Pub Date : 2023-12-16 DOI: 10.1016/j.engmic.2023.100135

Adigo Setargie , Chen Wang , Liwen Zhang , Yuquan Xu

{"title":"Chromatographic and Mass Spectroscopic Guided Discovery of Trichoderma Peptaibiotics and their Bioactivity","authors":"Adigo Setargie , Chen Wang , Liwen Zhang , Yuquan Xu","doi":"10.1016/j.engmic.2023.100135","DOIUrl":"10.1016/j.engmic.2023.100135","url":null,"abstract":"<div><p>Peptaibiotics are linear or cyclic peptide antibiotics characterized by the non-proteinogenic amino acid, alpha-aminoisobutyric acid. They exhibit a wide range of bioactivity against various pathogens. This report presents a comprehensive review of analytical methods for <em>Trichoderma</em> cultivation, production, isolation, screening, purification, and characterization of peptaibiotics, along with their bioactivity. Numerous techniques are currently available for each step, and we focus on describing the most commonly used and recently developed chromatographic and spectroscopic techniques. Investigating peptaibiotics requires efficient culture media, growth conditions, and isolation and purification techniques. The combination of chromatographic and spectroscopic tools offers a better opportunity for characterizing and identifying peptaibiotics. The evaluation of the chemical and biological properties of this compound has also been explored concerning its potential application in pharmaceutical and other industries. This review aims to summarize available data on the techniques and tools used to screen and purify peptaibiotics from <em>Trichoderma</em> fungi and bioactivity against various pathogens.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 2","pages":"Article 100135"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S266737032300067X/pdfft?md5=ae89c70326f4df088d4fe03f65e7a184&pid=1-s2.0-S266737032300067X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139026613","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}

引用次数: 0

Achieving simultaneous removal of carbon and nitrogen by an integrated process of anaerobic membrane bioreactor and flow-through biofilm reactor 通过厌氧膜生物反应器和流动生物膜反应器的综合工艺实现碳和氮的同步去除

Engineering Microbiology Pub Date : 2023-12-15 DOI: 10.1016/j.engmic.2023.100136

Xueshen Wu , Chao Wang , Depeng Wang , Ahmed Tawfik , Ronghua Xu , Zhong Yu , Fangang Meng

{"title":"Achieving simultaneous removal of carbon and nitrogen by an integrated process of anaerobic membrane bioreactor and flow-through biofilm reactor","authors":"Xueshen Wu , Chao Wang , Depeng Wang , Ahmed Tawfik , Ronghua Xu , Zhong Yu , Fangang Meng","doi":"10.1016/j.engmic.2023.100136","DOIUrl":"10.1016/j.engmic.2023.100136","url":null,"abstract":"<div><p>In this study, a combined system consisting of an anaerobic membrane bioreactor (AnMBR) and flow-through biofilm reactor/CANON (FTBR/CANON) was developed to simultaneously remove carbon and nitrogen from synthetic livestock wastewater. The average removal efficiencies of total nitrogen (TN) were 64.2 and 76.4% with influent ammonium (NH<sub>4</sub><sup>+</sup>-N) concentrations of approximately 200 and 500 mg/L, respectively. The COD removal efficiencies were higher than 98.0% during the entire operation. Mass balance analysis showed that COD and TN were mainly removed by the AnMBR and FTBR/CANON, respectively. The anammox process was the main nitrogen removal pathway in the combined system, with a contribution of over 80%. High functional bacterial activity was observed in the combined system. Particularly, an increase in the NH<sub>4</sub><sup>+</sup>-N concentration considerably improved the anammox activity of the biofilm in the FTBR/CANON. 16S rRNA high-throughput sequencing revealed that <em>Methanosaeta, Candidatus Methanofastidiosum</em>, and <em>Methanobacterium</em> were the dominant methanogens in the AnMBR granular sludge. In the CANON biofilm, <em>Nitrosomonas</em> and <em>Candidatus</em> Kuenenia were identified as aerobic and anaerobic ammonium-oxidizing bacteria, respectively. In summary, this study proposes a combined AnMBR and FTBR/CANON process targeting COD and nitrogen removal, and provides a potential alternative for treating high-strength wastewater.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100136"},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000681/pdfft?md5=8afe17500f65f7f5888c34f6b953307b&pid=1-s2.0-S2667370323000681-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139018324","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}

引用次数: 0

Rational design of a highly active N-glycosyltransferase mutant using fragment replacement approach 利用片段置换法合理设计高活性 N-糖基转移酶突变体

Engineering Microbiology Pub Date : 2023-11-30 DOI: 10.1016/j.engmic.2023.100134

Jiangyu Yang , Kun Li , Yongheng Rong , Zhaoxi Liu , Xiaoyu Liu , Yue Yu , Wenjing Shi , Yun Kong , Min Chen

{"title":"Rational design of a highly active N-glycosyltransferase mutant using fragment replacement approach","authors":"Jiangyu Yang , Kun Li , Yongheng Rong , Zhaoxi Liu , Xiaoyu Liu , Yue Yu , Wenjing Shi , Yun Kong , Min Chen","doi":"10.1016/j.engmic.2023.100134","DOIUrl":"10.1016/j.engmic.2023.100134","url":null,"abstract":"<div><p>The modularity of carbohydrate-active enzymes facilitates that enzymes with different functions have similar fragments. However, because of the complex structure of the enzyme active sites and the epistatic effects of various mutations on enzyme activity, it is difficult to design enzymes with multiple mutation sites using conventional methods. In this study, we designed multi-point mutants by fragment replacement in the donor-acceptor binding pocket of <em>Actinobacillus pleuropneumoniae N</em>-glycosyltransferase (ApNGT) to obtain novel properties. Candidate fragments were selected from a customized glycosyltransferase database. The stability and substrate-binding energy of the three fragment replacement mutants were calculated in comparison with wild-type ApNGT, and mutants with top-ranking stability and middle-ranking substrate-binding energy were chosen for priority experimental verification. We found that a mutant called F13, which increased the glycosylation efficiency of the natural substrate by 1.44 times, the relative conversion of UDP-galactose by 14.2 times, and the relative conversion of UDP-xylose from almost 0 to 78.6%. Most importantly, F13 mutant acquired an entirely new property, the ability to utilize UDP-glucuronic acid. On one hand, this work shows that replacing similar fragments in the donor-acceptor binding pocket of the enzyme might provide new ideas for designing mutants with new properties; on the other hand, F13 mutant is expected to play an important role in targeted drug delivery.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100134"},"PeriodicalIF":0.0,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000668/pdfft?md5=9d882243453dbe21a97fd045b480ba38&pid=1-s2.0-S2667370323000668-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139297743","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}

引用次数: 0

Erratum regarding missing statements in previously published articles 关于先前发表的文章中缺失陈述的勘误

Engineering Microbiology Pub Date : 2023-11-16 DOI: 10.1016/j.engmic.2023.100125

引用次数: 0

Metabolic engineering: Tools and applications 代谢工程:工具和应用

Engineering Microbiology Pub Date : 2023-11-04 DOI: 10.1016/j.engmic.2023.100126

Yun Chen , Jiazhang Lian , Jin Hou

引用次数: 0

Exploring the diversity of microbes and natural products from fungus-growing termite tripartite symbiosis 探索真菌与白蚁三方共生中微生物和天然产物的多样性

Engineering Microbiology Pub Date : 2023-11-04 DOI: 10.1016/j.engmic.2023.100124

Muhammad Shoaib , Ruining Bai , Shuai Li , Yan Xie , Yulong Shen , Jinfeng Ni

{"title":"Exploring the diversity of microbes and natural products from fungus-growing termite tripartite symbiosis","authors":"Muhammad Shoaib , Ruining Bai , Shuai Li , Yan Xie , Yulong Shen , Jinfeng Ni","doi":"10.1016/j.engmic.2023.100124","DOIUrl":"10.1016/j.engmic.2023.100124","url":null,"abstract":"<div><p>The fungus-growing termite is considered a distinct ecological niche because it involves a tripartite symbiosis between the termite host, gut microflora, and the <em>in vitro</em> fungus <em>Termitomyces</em>, which has led to the expansion of highly organized and complex societies among termite colonies. Tripartite symbiosis in fungus-growing termites may promote unique microbes with distinctive metabolic pathways that may serve as valuable resources for developing novel antimicrobial therapeutic options. Recent research on complex tripartite symbioses has revealed a plethora of previously unknown natural products that may have ecological roles in signaling, communication, or defense responses. Natural products produced by symbionts may act as crucial intermediaries between termites and their pathogens by providing direct protection through their biological activities. Herein, we review the state-of-the-art research on both microbes and natural products originated from fungus-growing termite tripartite symbiosis, highlighting the diversity of microbes and the uniqueness of natural product classes and their bioactivities. Additionally, we emphasize future research prospects on fungus-growing termite related microorganisms, with a particular focus on their potential roles in bioactive product discovery.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100124"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000565/pdfft?md5=626d1e0eddd0b16494e5e73d294b7fe8&pid=1-s2.0-S2667370323000565-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135455640","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}

引用次数: 0

Advances and applications of CRISPR/Cas-mediated interference in Escherichia coli 大肠杆菌中 CRISPR/Cas 介导的干扰的进展与应用

Engineering Microbiology Pub Date : 2023-11-02 DOI: 10.1016/j.engmic.2023.100123

Xiaohui Lim, Congqiang Zhang, Xixian Chen

{"title":"Advances and applications of CRISPR/Cas-mediated interference in Escherichia coli","authors":"Xiaohui Lim, Congqiang Zhang, Xixian Chen","doi":"10.1016/j.engmic.2023.100123","DOIUrl":"10.1016/j.engmic.2023.100123","url":null,"abstract":"<div><p>The bacterium <em>Escherichia coli</em> (<em>E. coli</em>) is one of the most widely used chassis microbes employed for the biosynthesis of numerous valuable chemical compounds. In the past decade, the metabolic engineering of <em>E. coli</em> has undergone significant advances, although further productivity improvements will require extensive genome modification, multi-dimensional regulation, and multiple metabolic-pathway coordination. In this context, clustered regularly interspaced short palindromic repeats (CRISPR), along with CRISPR-associated protein (Cas) and its inactive variant (dCas), have emerged as notable recombination and transcriptional regulation tools that are particularly useful for multiplex metabolic engineering in <em>E. coli</em>. In this review, we briefly describe the CRISPR/Cas9 technology in <em>E. coli</em>, and then summarize the recent advances in CRISPR/dCas9 interference (CRISPRi) systems in <em>E. coli</em>, particularly the strategies designed to effectively regulate gene repression and overcome retroactivity during multiplexing. Moreover, we discuss recent applications of the CRISPRi system for enhancing metabolite production in <em>E. coli</em>, and finally highlight the major challenges and future perspectives of this technology.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100123"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000553/pdfft?md5=4d0cbb9f9fc0584a0733f98e22ad4832&pid=1-s2.0-S2667370323000553-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135371231","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}

引用次数: 0

Engineering Saccharomyces cerevisiae for efficient production of recombinant proteins 改造酿酒酵母，高效生产重组蛋白质

Engineering Microbiology Pub Date : 2023-10-12 DOI: 10.1016/j.engmic.2023.100122

Shuo Yang , Liyun Song , Jing Wang , Jianzhi Zhao , Hongting Tang , Xiaoming Bao

{"title":"Engineering Saccharomyces cerevisiae for efficient production of recombinant proteins","authors":"Shuo Yang , Liyun Song , Jing Wang , Jianzhi Zhao , Hongting Tang , Xiaoming Bao","doi":"10.1016/j.engmic.2023.100122","DOIUrl":"10.1016/j.engmic.2023.100122","url":null,"abstract":"<div><p><em>Saccharomyces cerevisiae</em> is an excellent microbial cell factory for producing valuable recombinant proteins because of its fast growth rate, robustness, biosafety, ease of operability via mature genomic modification technologies, and the presence of a conserved post-translational modification pathway among eukaryotic organisms. However, meeting industrial and market requirements with the current low microbial production of recombinant proteins can be challenging. To address this issue, numerous efforts have been made to enhance the ability of yeast cell factories to efficiently produce proteins. In this review, we provide an overview of recent advances in <em>S. cerevisiae</em> engineering to improve recombinant protein production. This review focuses on the strategies that enhance protein production by regulating transcription through promoter engineering, codon optimization, and expression system optimization. Additionally, we describe modifications to the secretory pathway, including engineered protein translocation, protein folding, glycosylation modification, and vesicle trafficking. Furthermore, we discuss global metabolic pathway optimization and other relevant strategies, such as the disruption of protein degradation, cell wall engineering, and random mutagenesis. Finally, we provide an outlook on the developmental trends in this field, offering insights into future directions for improving recombinant protein production in <em>S. cerevisiae</em>.</p></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"4 1","pages":"Article 100122"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667370323000541/pdfft?md5=09024df4a0818d7b3b48953b72932856&pid=1-s2.0-S2667370323000541-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136118606","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}

引用次数: 0