Current opinion in microbiology最新文献

The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes.

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2025-01-22 DOI: 10.1016/j.mib.2025.102580

Shreya Arya, Ashish B George, James O'Dwyer

{"title":"The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes.","authors":"Shreya Arya, Ashish B George, James O'Dwyer","doi":"10.1016/j.mib.2025.102580","DOIUrl":"https://doi.org/10.1016/j.mib.2025.102580","url":null,"abstract":"Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models - a middle, third way for using theory to inform design.","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"102580"},"PeriodicalIF":5.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dissecting S-itaconation at host-pathogen interactions with chemical proteomics tools.

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2025-01-21 DOI: 10.1016/j.mib.2025.102579

Zihua Liu, Chu Wang

引用次数: 0

Harnessing gut microbial communities to unravel microbiome functions. 利用肠道微生物群落来揭示微生物群的功能。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2025-01-08 DOI: 10.1016/j.mib.2024.102578

Samir Giri, Handuo Shi, Athanasios Typas, Kerwyn Casey Huang

{"title":"Harnessing gut microbial communities to unravel microbiome functions.","authors":"Samir Giri, Handuo Shi, Athanasios Typas, Kerwyn Casey Huang","doi":"10.1016/j.mib.2024.102578","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102578","url":null,"abstract":"The gut microbiome impacts human health in direct and indirect ways. While many associations have been discovered between specific microbiome compositions and diseases, establishing causality, understanding the underlying mechanisms, and developing successful microbiome-based therapies require novel experimental approaches. In this opinion, we discuss how in vitro cultivation of diverse communities enables systematic investigation of the individual and collective functions of gut microbes. Up to now, the field has relied mostly on simple, bottom-up assembled synthetic communities or more complex, undefined stool-derived communities. Although powerful for dissecting interactions and mapping causal effects, these communities suffer either from ignoring the complexity, diversity, coevolution, and dynamics of natural communities or from lack of control of community composition. These limitations can be overcome in the future by establishing personalized culture collections from stool samples of different donors and assembling personalized communities to investigate native interactions and ecological relationships in a controlled manner.","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"102578"},"PeriodicalIF":5.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142946135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A CRISPR view on genetic screens in Toxoplasma gondii. 刚地弓形虫基因筛选的CRISPR观点。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2025-01-07 DOI: 10.1016/j.mib.2024.102577

Franziska Hildebrandt, Ana N Matias, Moritz Treeck

引用次数: 0

Revisiting the potential of natural products in antimycobacterial therapy: advances in drug discovery and semisynthetic solutions. 重新审视天然产物在抗细菌治疗中的潜力：药物发现和半合成解决方案的进展。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-31 DOI: 10.1016/j.mib.2024.102576

Maya George, Gerard D Wright

{"title":"Revisiting the potential of natural products in antimycobacterial therapy: advances in drug discovery and semisynthetic solutions.","authors":"Maya George, Gerard D Wright","doi":"10.1016/j.mib.2024.102576","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102576","url":null,"abstract":"Natural products have been pivotal in treating mycobacterial infections with early antibiotics such as streptomycin, forming the foundation of tuberculosis therapy. However, the emergence of multidrug-resistant and extensively drug-resistant Mycobacterium species has intensified the need for novel antimycobacterial agents. In this review, we revisit the historical contributions of natural products to antimycobacterial drug discovery and highlight recent advances in the field. We assess the application of molecular networking and the exploration of unculturable bacteria in identifying new antimycobacterial compounds such as amycobactin and levesquamides. We also highlight the role of semisynthesis in optimizing natural products, exemplified by sequanamycins and spectinomycin analogs that evade M. tuberculosis' intrinsic resistance. Finally, we discuss emerging technologies that are promising to accelerate the discovery and development of next-generation antimycobacterial therapies. Despite ongoing challenges, these innovative approaches offer renewed hope in addressing the growing crisis of drug-resistant mycobacterial infections.","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"102576"},"PeriodicalIF":5.9,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Innovative approaches in the discovery of terpenoid natural products. 发现萜类天然产物的创新方法。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-20 DOI: 10.1016/j.mib.2024.102575

Shu Cheng, Xinghuan Wang, Zixin Deng, Tiangang Liu

引用次数: 0

Dirammox (direct ammonia oxidation) to nitrogen (N₂): discovery, current status, and perspectives. 地拉莫克斯（氨直接氧化）制氮（N2）：发现、现状和前景。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-10 DOI: 10.1016/j.mib.2024.102565

Ji-Guo Qiu, Shuang-Jiang Liu

{"title":"Dirammox (direct ammonia oxidation) to nitrogen (N2): discovery, current status, and perspectives.","authors":"Ji-Guo Qiu, Shuang-Jiang Liu","doi":"10.1016/j.mib.2024.102565","DOIUrl":"https://doi.org/10.1016/j.mib.2024.102565","url":null,"abstract":"Microbial ammonia oxidation plays an important role in nitrogen (N2) cycling in natural and man-made systems. Heterotrophic microorganisms that oxidize ammonia were observed more than a century ago; however, the underlying molecular mechanism of ammonia oxidation is still mysterious. Dirammox (direct ammonia oxidation to N2) is a newly described heterotrophic ammonia oxidation process in which ammonia or its organic amine is oxidized into hydroxylamine and then directly converted to N2 gas without the involvement of nitrite and nitrate. As demonstrated with Alcaligenes species, the conversion of ammonia to hydroxylamine is mediated by the dnf genes, and hydroxylamine conversion to N2 is considered both a biotic and abiotic process. Dirammox is different from the N2-producing processes of nitrification-denitrification and anaerobic ammonia oxidation (anammox), in which nitrite or nitrate is involved. Here, we review the discovery of dirammox, progress toward understanding its genetics, biochemistry, physiology, and ecology, and future perspectives and directions.","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"83 ","pages":"102565"},"PeriodicalIF":5.9,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alginate catabolic systems in marine bacteria. 海藻酸盐在海洋细菌中的分解代谢系统。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-09 DOI: 10.1016/j.mib.2024.102564

Fei Xu, Xiu-Lan Chen, Yu-Zhong Zhang

引用次数: 0

The promise of CRISPR-associated transposons for bacterial functional genomics. crispr相关转座子在细菌功能基因组学中的应用前景。

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-03 DOI: 10.1016/j.mib.2024.102563

Amy B Banta, Rodrigo A Cuellar, Nischala Nadig, Bryce C Davis, Jason M Peters

引用次数: 0

Animating insights into the biosynthesis of glycopeptide antibiotics 对糖肽抗生素生物合成的生动见解

IF 5.9 2区生物学

Current opinion in microbiology Pub Date : 2024-12-01 DOI: 10.1016/j.mib.2024.102561

Athina Gavriilidou , Martina Adamek , Jens-Peter Rodler , Noel Kubach , Anna Voigtländer , Leon Kokkoliadis , Chambers C Hughes , Max J Cryle , Evi Stegmann , Nadine Ziemert

{"title":"Animating insights into the biosynthesis of glycopeptide antibiotics","authors":"Athina Gavriilidou , Martina Adamek , Jens-Peter Rodler , Noel Kubach , Anna Voigtländer , Leon Kokkoliadis , Chambers C Hughes , Max J Cryle , Evi Stegmann , Nadine Ziemert","doi":"10.1016/j.mib.2024.102561","DOIUrl":"10.1016/j.mib.2024.102561","url":null,"abstract":"<div><div>The realm of natural product (NP) research is constantly expanding, with diverse applications in both medicine and industry. In this interdisciplinary field, scientists collaborate to investigate various aspects of NPs, including understanding the mode of action of these compounds, unraveling their biosynthetic pathways, studying evolutionary aspects, and biochemically characterizing the enzymes involved. However, this collaboration can be challenging as all parties involved come from very different backgrounds (such as microbiology, synthetic chemistry, biochemistry, or bioinformatics) and may not use the same terminology. Fortunately, contemporary technologies, such as videos, provide novel avenues for effective engagement. Recognizing the potency of visual stimuli in explaining complex processes, we envision a future where animations become more and more common in interdisciplinary communication, accompanying perspectives, and reviews. To demonstrate how such approaches can enhance the understanding of complex processes, we have animated the biosynthesis of the glycopeptide antibiotic vancomycin (https://youtu.be/TGAgC4c8hvo).</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"82 ","pages":"Article 102561"},"PeriodicalIF":5.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142745854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0