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Current Opinion in Systems Biology最新文献

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Microbial production of fuels, commodity chemicals, and materials from sustainable sources of carbon and energy 微生物生产的燃料，商品化学品和材料从可持续的碳和能源来源
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-10-31 DOI: 10.1016/j.coisb.2023.100482
Aidan E. Cowan , Sarah H. Klass , Peter H. Winegar , Jay D. Keasling
{"title":"Microbial production of fuels, commodity chemicals, and materials from sustainable sources of carbon and energy","authors":"Aidan E. Cowan ,&nbsp;Sarah H. Klass ,&nbsp;Peter H. Winegar ,&nbsp;Jay D. Keasling","doi":"10.1016/j.coisb.2023.100482","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100482","url":null,"abstract":"<div><p>Anthropogenic carbon emissions are driving rapid changes to the earth's climate, disrupting whole ecosystems and endangering the stability of human society. Innovations in engineered microbial fermentation enable the fossil resource-free production of fuels, commodity chemicals, and materials, thereby reducing the carbon emissions associated with these products. Microorganisms have been engineered to catabolize sustainable sources of carbon and energy (<em>i.e.</em>, plant biomass, plastic waste, and one-carbon feedstocks) and biosynthesize carbon-neutral or carbon-negative products. These engineering efforts exploit and optimize natural biological pathways or generate unnatural pathways which can biosynthesize chemicals that have not yet been accessed using synthetic chemistry. Recent advances in microbial fermentation seek not only to maximize the titer, rate, and yield of desired products, but also to tailor microbial catabolism to utilize inexpensive feedstocks. Ultimately, these advances aim to lower the cost of bioproduction so that microorganism-derived chemicals can be economically competitive with fossil-derived chemicals.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100482"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136571775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution 微生物在自然界中是如何生长的?种群动态在微生物生态学和进化中的作用
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-08-09 DOI: 10.1016/j.coisb.2023.100470
Justus Wilhelm Fink , Michael Manhart
{"title":"How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution","authors":"Justus Wilhelm Fink ,&nbsp;Michael Manhart","doi":"10.1016/j.coisb.2023.100470","DOIUrl":"10.1016/j.coisb.2023.100470","url":null,"abstract":"<div><p>The growth of microbial populations in nature is dynamic, as the cellular physiology and environment of these populations change. Population dynamics have wide-ranging consequences for ecology and evolution, determining how species interact and which mutations fix. Understanding these dynamics is also critical for clinical and environmental applications in which we need to promote or inhibit microbial growth<span>. We first address the latest efforts and outstanding challenges in measuring microbial population dynamics in natural environments. We next summarize fundamental concepts and empirical data on how population dynamics both shape and are shaped by evolutionary processes. Finally, we discuss the role of tradeoffs in microbial population dynamics, which may reveal physiological constraints and help to maintain ecological diversity. We find that current evidence for tradeoffs in population dynamics is limited, but that consideration of the evolutionary context of these tradeoffs is necessary for designing future experiments that can better address this problem.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100470"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42046217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Advances in engineering genetic circuits for microbial biocontainment 微生物控制工程基因电路的研究进展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-11-04 DOI: 10.1016/j.coisb.2023.100483
Yuefeng Ma , Abhijit Manna , Tae Seok Moon
{"title":"Advances in engineering genetic circuits for microbial biocontainment","authors":"Yuefeng Ma ,&nbsp;Abhijit Manna ,&nbsp;Tae Seok Moon","doi":"10.1016/j.coisb.2023.100483","DOIUrl":"10.1016/j.coisb.2023.100483","url":null,"abstract":"<div><p><span>The development of synthetic biology has resulted in the use of genetically engineered microbes<span> (GEMs), becoming increasingly critical for addressing global issues such as health, food shortage, climate crisis, and environmental pollution. However, GEMs also pose a potential threat to the ecosystem, necessitating the implementation of biocontainment strategies. Synthetic genetic circuits have the potential to provide an additional level of safety and control beyond traditional physical containment measures. The development of biocontainment strategies is ongoing, including the use of kill switches, </span></span>auxotrophy, and stringent response circuits, to control the viability of GEMs. This review discusses the application and future directions of genetic circuits for microbial biocontainment strategies.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100483"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135454736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial Board Page 编辑委员会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-12-05 DOI: 10.1016/S2452-3100(23)00052-5
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(23)00052-5","DOIUrl":"https://doi.org/10.1016/S2452-3100(23)00052-5","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100495"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310023000525/pdfft?md5=796aff2b175ba2c293085564fefc486e&pid=1-s2.0-S2452310023000525-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138489626","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
Robustness of microbiome function 微生物组功能的稳健性
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-09-14 DOI: 10.1016/j.coisb.2023.100479
Kiseok Keith Lee , Yeonwoo Park , Seppe Kuehn
{"title":"Robustness of microbiome function","authors":"Kiseok Keith Lee ,&nbsp;Yeonwoo Park ,&nbsp;Seppe Kuehn","doi":"10.1016/j.coisb.2023.100479","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100479","url":null,"abstract":"<div><p><span>Microbial communities perform metabolic processes that sustain life on Earth and promote human health. Microbial consortia sustain these functions in the face of constant structural and environmental perturbations. How do complex communities robustly sustain their functional properties despite perturbations? Most studies of functional robustness in the </span>microbiome have been limited to biodiversity and functional redundancy, the idea that there are multiple members of the community that can sustain a specific function. Here, we propose that ideas from other complex biological systems may be applied to deepen our understanding of microbiome robustness. By surveying the causes of functional robustness in a variety of biological systems, including proteins and cells, and discussing how they can be applied to the microbiome, we build conceptual and experimental frameworks for understanding the functional robustness of microbial communities. We hope that these insights might help better predict and engineer microbiome function.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100479"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50173551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Recent advances in non-model bacterial chassis construction 非模型细菌底盘结构研究进展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-08-19 DOI: 10.1016/j.coisb.2023.100471
Soonkyu Hwang , Chanyoung Joung , Woori Kim , Bernhard Palsson , Byung-Kwan Cho
{"title":"Recent advances in non-model bacterial chassis construction","authors":"Soonkyu Hwang ,&nbsp;Chanyoung Joung ,&nbsp;Woori Kim ,&nbsp;Bernhard Palsson ,&nbsp;Byung-Kwan Cho","doi":"10.1016/j.coisb.2023.100471","DOIUrl":"10.1016/j.coisb.2023.100471","url":null,"abstract":"<div><p>The development of bacterial chassis to increase productivity and reduce industrial costs in value-added biochemical production has gained significant attention. Current efforts have focused on model bacteria, thus limiting their suitability to produce specialized products. Therefore, there is a growing emphasis on developing specialized non-model bacterial chassis to expand the repertoire of bioproducts. However, the lack of genetic information and tools for non-model bacteria remains challenging. In this review, we categorize and introduce non-model chassis based on their characteristics in relation to the target products. We also provide an overview of the trends in the development of genome-reduced chassis to enhance productivity. Furthermore, we propose synthetic biology technologies that can be applied to a broad range of non-model bacteria.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100471"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43537194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Evolution of new metabolic pathways and microbial communities 新代谢途径和微生物群落的进化
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-08-25 DOI: 10.1016/j.coisb.2023.100472
Dan Kehila, Kimberly Tsz Ching Wong, Nobuhiko Tokuriki
{"title":"Evolution of new metabolic pathways and microbial communities","authors":"Dan Kehila,&nbsp;Kimberly Tsz Ching Wong,&nbsp;Nobuhiko Tokuriki","doi":"10.1016/j.coisb.2023.100472","DOIUrl":"10.1016/j.coisb.2023.100472","url":null,"abstract":"<div><p>The evolution of metabolic pathways in microbes is traditionally envisioned to take place within a single organism. The diverse repertoire of enzymes in the microbial community points to another exciting possibility: namely, that new metabolic pathways may evolve in a community setting, where pathway steps are distributed across several strains. The readiness with which microbes form stable relationships to collectively degrade manmade ‘xenobiotic’ pollutants, as evidenced from natural and laboratory-enriched consortia, provides valuable insights into the evolution of enzymes and pathways. Nonetheless, many open questions remain to be addressed. In this review, we consider the key determinants of pathway evolution in microbial communities, drawing from principles of social evolutionary theory in microbes, and also exploring the role of diffusion and horizontal gene transfer.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100472"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45099772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Shedding light on spatial structure and dynamics in phototrophic biofilms 揭示光养生物膜的空间结构和动态
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-10-06 DOI: 10.1016/j.coisb.2023.100480
Freddy Bunbury, Amanda N. Shelton, Devaki Bhaya
{"title":"Shedding light on spatial structure and dynamics in phototrophic biofilms","authors":"Freddy Bunbury,&nbsp;Amanda N. Shelton,&nbsp;Devaki Bhaya","doi":"10.1016/j.coisb.2023.100480","DOIUrl":"https://doi.org/10.1016/j.coisb.2023.100480","url":null,"abstract":"<div><p><span>Microbial phototrophic communities dominated early Earth and thrive to this day, particularly in extreme environments. We focus on the impact of diel oscillations on phototrophic biofilms, especially in hot springs, where oxygenic phototrophs are keystone species that use light energy to fix carbon and often nitrogen. They exhibit photo-motility and stratification, and alter the physicochemical environment by driving O</span><sub>2</sub>, CO<sub>2,</sub><span> and pH oscillations. Omics analyses reveal extensive genomic and functional diversity in biofilms, but linking this to a predictive understanding of their structure and dynamics remains challenging. This can be addressed by better spatiotemporal resolution of microbial interactions, improved tools for building and manipulating synthetic communities, and integration of empirical and theoretical approaches.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100480"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90029760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A pan-metazoan view of germline-soma distinction challenges our understanding of how the metazoan germline evolves 泛后生动物对生殖细胞-体细胞区分的观点挑战了我们对后生动物生殖细胞如何进化的理解
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-12-01 Epub Date: 2023-11-11 DOI: 10.1016/j.coisb.2023.100486
Dominic K. Devlin , Austen R.D. Ganley , Nobuto Takeuchi
{"title":"A pan-metazoan view of germline-soma distinction challenges our understanding of how the metazoan germline evolves","authors":"Dominic K. Devlin ,&nbsp;Austen R.D. Ganley ,&nbsp;Nobuto Takeuchi","doi":"10.1016/j.coisb.2023.100486","DOIUrl":"10.1016/j.coisb.2023.100486","url":null,"abstract":"<div><p>A germline-soma distinction — irreversible differentiation from reproductive germline cells to sterile somatic cells — is a landmark of cellular cooperation in metazoans. Traditionally, this distinction was considered a property of only some metazoan taxa, such as vertebrates and insects. However, recent studies on a number of other metazoan taxa are challenging this traditional perspective, suggesting that a germline-soma distinction is widespread among metazoans. Here, we review recent molecular and cellular evidence supporting this suggestion and emphasise the difference between germline-soma distinction and germline segregation. We also outline the considerable diversity among metazoans in germline specification, segregation and regeneration. We finish by discussing how evolutionary explanations for this diversity can be investigated by harnessing theoretical modelling approaches.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100486"},"PeriodicalIF":3.7,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310023000434/pdfft?md5=06baf838b4701fd9a8bb16f2bc11278d&pid=1-s2.0-S2452310023000434-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135668926","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
Prophage mediated control of higher order interactions - Insights from multi-level approaches 噬菌体介导的高阶相互作用的控制——来自多层次方法的见解
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-09-01 Epub Date: 2023-06-28 DOI: 10.1016/j.coisb.2023.100469
Carolin C. Wendling
{"title":"Prophage mediated control of higher order interactions - Insights from multi-level approaches","authors":"Carolin C. Wendling","doi":"10.1016/j.coisb.2023.100469","DOIUrl":"10.1016/j.coisb.2023.100469","url":null,"abstract":"<div><p><span>Prophages, latent viral elements residing in </span>bacterial genomes<span> affect bacterial ecology and evolution in diverse ways. Do these prophage-mediated effects extend beyond the prophage-bacterial relationship? Here, I summarize the latest advances exploring how the impacts of prophages are transmitted through multiple levels of biological systems with potential impacts on ecosystem stability and functioning. The diverse effects of prophages on higher-order interactions are context-specific, ranging from contributions to global biogeochemical processes and mutualistic interactions to increased disease severity with negative impacts on ecosystem engineers and potential cascading effects for multiple species. While we have a solid understanding of the mechanisms by which prophages modulate their bacterial hosts at the cellular and population levels, future research may take an integrative approach to quantify their effects in complex ecosystems.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"35 ","pages":"Article 100469"},"PeriodicalIF":3.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47770957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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