Current opinion in microbiology最新文献_第2页

Applicability of synthetic communities of the infant gut microbiota to understand microbial dynamics in an interchanging glycan landscape 婴儿肠道微生物群的合成群落的适用性，以了解相互交换的聚糖景观中的微生物动力学

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-30 DOI: 10.1016/j.mib.2025.102659

Athanasia Ioannou, Clara Belzer

引用次数: 0

Decoding the epigenetic blueprint behind Toxoplasma (pre)sexual commitment and chronic persistence 破译弓形虫（前）性承诺和慢性持久性背后的表观遗传蓝图

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-30 DOI: 10.1016/j.mib.2025.102662

Martina Shahinas, Belen Pachano, Marie G Robert, Christopher Swale, Mohamed-Ali Hakimi

{"title":"Decoding the epigenetic blueprint behind Toxoplasma (pre)sexual commitment and chronic persistence","authors":"Martina Shahinas, Belen Pachano, Marie G Robert, Christopher Swale, Mohamed-Ali Hakimi","doi":"10.1016/j.mib.2025.102662","DOIUrl":"10.1016/j.mib.2025.102662","url":null,"abstract":"<div><div><em>Toxoplasma gondii</em>, a widespread apicomplexan parasite, navigates a complex life cycle in which it switches back and forth between tachyzoites and bradyzoites to balance acute infection and persistence while also undergoing an often-overlooked one-way commitment to the sexual stage. Emerging evidence suggests that <em>Toxoplasma</em>’s developmental trajectories are orchestrated by an interconnected network of transcriptional switches and chromatin remodeling mechanisms, acting in concert to ensure robust stage transitions. This review outlines an updated epigenetic framework for stage transitions and highlights the functional synergy between an Imitation SWItch family chromatin remodeler and the MORC/HDAC3 repressor complex, which together modulate chromatin accessibility to maintain or shift developmental states. We also spotlight recent findings, showing that simultaneous depletion of AP2XII-1 and AP2XI-2 transcription factors reactivates the presexual program <em>in vitro</em>, eliminating the need for cat hosts and allowing ethical, scalable exploration of sexual stages. Strikingly, the knockdown of these transcription factors also reveals a previously unrecognized hybrid zoite co-expressing bradyzoite and merozoite markers, suggesting a transitional state that defies classical stage definition. This hybrid form, as well as more recent data on bradyzoite development, support a new model in which <em>T. gondii</em> development unfolds along a continuum of epigenetically primed states rather than a rigid sequence of binary fate decisions. These findings provide a powerful conceptual and experimental framework for dissecting parasite transmission and persistence and have far-reaching implications for the biology of other parasites in the phylum.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"88 ","pages":"Article 102662"},"PeriodicalIF":7.5,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916905","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

Structuring complexity by mapping the possible in microbial ecosystems 通过绘制微生物生态系统中的可能性来构建复杂性

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-28 DOI: 10.1016/j.mib.2025.102658

Djordje Bajić, Marco van Oort, Minke Gabriëls, Uroš Gojković

{"title":"Structuring complexity by mapping the possible in microbial ecosystems","authors":"Djordje Bajić, Marco van Oort, Minke Gabriëls, Uroš Gojković","doi":"10.1016/j.mib.2025.102658","DOIUrl":"10.1016/j.mib.2025.102658","url":null,"abstract":"<div><div>Microbial ecosystems consist of many interacting components that integrate through stochastic and highly dynamic processes across multiple scales. Yet, despite this complexity, microbial communities exhibit remarkably robust patterns and reproducible functions. This apparent paradox reflects the role of constraints, whether physical, physiological, or evolutionary, that channel stochasticity into structured outcomes. Due to the limited knowledge of the nature of these constraints, models in ecology have traditionally relied on stochastic exploration under minimal mechanistic assumptions. Now, advances in data availability and computational methods increasingly allow us to construct models that incorporate explicit mechanistic constraints. In this review, we synthesize emerging modeling approaches that explore the space of ecological possibility in microbial ecosystems under realistic constraints, such as those imposed by metabolic stoichiometry, thermodynamics, or the structure of ecological interaction networks. We argue that integrating such constraints can significantly improve the predictive resolution of models, helping us build a much needed bridge between theory and data. We further discuss how novel statistical approaches are revealing simple, low-dimensional patterns in microbial communities, offering empirical clues for identifying the underlying constraints. Together, these developments suggest a path toward a data-driven and mechanistically informed theory in microbial ecology.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"88 ","pages":"Article 102658"},"PeriodicalIF":7.5,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144912632","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

Taming wild replicons: evolution and domestication of large extrachromosomal replicons 驯化野生复制子：进化和驯化大型染色体外复制子

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-19 DOI: 10.1016/j.mib.2025.102657

Ostermayer Jasmin , Guzzi Noa , Czarnecki Jakub , Soler-Bistué Alfonso , Mazel Didier , Val Marie-Eve

{"title":"Taming wild replicons: evolution and domestication of large extrachromosomal replicons","authors":"Ostermayer Jasmin , Guzzi Noa , Czarnecki Jakub , Soler-Bistué Alfonso , Mazel Didier , Val Marie-Eve","doi":"10.1016/j.mib.2025.102657","DOIUrl":"10.1016/j.mib.2025.102657","url":null,"abstract":"<div><div>Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as megaplasmids, secondary chromosomes, or chromids. Multipartite genomes, which include large ERs, are present in approximately 10% of sequenced bacterial species and are thought to have evolved as adaptive solutions to diverse ecological niches. Understanding how these replicons become essential genome components is critical for characterizing bacterial adaptability and genome plasticity. Large ERs become established within the host genome through evolutionary processes that shape their genetic content, promote the acquisition of core functions, and synchronize their replication and segregation with the bacterial cell cycle. In this review, we examine the origin, classification, and functional roles of large ERs. We highlight shared maintenance principles, such as dosage-dependent gene organization, replication control via methylation or checkpoint mechanisms, and dedicated partitioning systems or shared segregation machinery. Examples from <em>Vibrio cholerae</em> and <em>Agrobacterium tumefaciens</em> illustrate these mechanisms, and a conceptual model for ER domestication is proposed.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"88 ","pages":"Article 102657"},"PeriodicalIF":7.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863648","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

Structure, function, and quantitative biology of the Drosophila gut microbiome 果蝇肠道微生物群的结构、功能和定量生物学

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-18 DOI: 10.1016/j.mib.2025.102653

William B Ludington , Haolong Zhu , Kevin Aumiller , Angela Xu , Josh Derrick

引用次数: 0

Circadian interactions between plants and microorganisms 植物和微生物之间的昼夜相互作用

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-15 DOI: 10.1016/j.mib.2025.102655

Jack Dorling, Georgia Love, Isobel K. Banks, Antony N. Dodd

{"title":"Circadian interactions between plants and microorganisms","authors":"Jack Dorling, Georgia Love, Isobel K. Banks, Antony N. Dodd","doi":"10.1016/j.mib.2025.102655","DOIUrl":"10.1016/j.mib.2025.102655","url":null,"abstract":"<div><div>Life on Earth evolved in environmental conditions that fluctuate with a daily cycle. Organisms from all kingdoms of life, including plants and their associated microorganisms, harbour circadian clocks as an adaptation to these environmental changes. We review the involvement of circadian clocks in associations between plants and microbes, focusing first on mechanisms of specific circadian clock-regulated plant–microbe interactions. We then discuss more general ecological and evolutionary consequences of clock regulation of plant–microbe interactions and argue that circadian clocks can choreograph complex plant–microbe community interactions across multiple levels of biological organisation. We also discuss the difficulties in determining the precise nature of interactions in such communities, for both individual rhythmic interactions and the emergent rhythmic properties of these communities. An understanding of the regulation of these interactions by circadian clocks is likely to have implications for crop performance, fertiliser and pesticide use, soil and ecosystem health, biogeochemical cycling, and the impacts of global warming.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"88 ","pages":"Article 102655"},"PeriodicalIF":7.5,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841909","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

Investigating bacterial evolution in nature with metagenomics 用宏基因组学研究自然界中的细菌进化

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-13 DOI: 10.1016/j.mib.2025.102654

Abigayle MR Simpson , Alexander B Chase , Alejandra Rodríguez-Verdugo , Jennifer BH Martiny

{"title":"Investigating bacterial evolution in nature with metagenomics","authors":"Abigayle MR Simpson , Alexander B Chase , Alejandra Rodríguez-Verdugo , Jennifer BH Martiny","doi":"10.1016/j.mib.2025.102654","DOIUrl":"10.1016/j.mib.2025.102654","url":null,"abstract":"<div><div>Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate <em>in situ</em> evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome’s response to environmental change.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"87 ","pages":"Article 102654"},"PeriodicalIF":7.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144827117","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

Engineering natural microbial communities: harnessing synthetic communities for bioremediation 工程天然微生物群落：利用合成群落进行生物修复

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-08-05 DOI: 10.1016/j.mib.2025.102652

Chen Chen, Kunyao Li, Xinyu Lin, Wanxin Li, Xihui Xu

{"title":"Engineering natural microbial communities: harnessing synthetic communities for bioremediation","authors":"Chen Chen, Kunyao Li, Xinyu Lin, Wanxin Li, Xihui Xu","doi":"10.1016/j.mib.2025.102652","DOIUrl":"10.1016/j.mib.2025.102652","url":null,"abstract":"<div><div>Microbial bioremediation, a technology using microbial metabolism to degrade or transform environmental pollutants, has garnered significant attention in recent years due to its eco-friendly and cost-effective advantages. In comparison with traditional single-strain-based bioremediation, microbial communities can remarkably enhance bioremediation. However, natural microbial communities are not optimally structured for bioremediation purposes. Given that the composition and structure of a microbial community directly influence the efficiency and pathway of pollutant metabolism, the artificial design of microbial communities is of great significance for improving bioremediation. Synthetic communities (SynComs), as artificially designed microbial consortia, can significantly enhance bioremediation efficiency and environmental adaptability through metabolic interactions among their constituent strains. Constructing SynComs generally requires a precise design of their composition and structure to optimize their metabolic functions. Here, we review the mechanisms by which SynComs enhance bioremediation, the prevalent strategies for constructing SynComs, and the latest advancements in metabolic modeling techniques for SynCom design.</div></div>","PeriodicalId":10921,"journal":{"name":"Current opinion in microbiology","volume":"87 ","pages":"Article 102652"},"PeriodicalIF":7.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144780093","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

Assembly and maturation of methyl-coenzyme M reductase in methanogenic archaea 产甲烷古菌中甲基辅酶M还原酶的组装和成熟

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-07-29 DOI: 10.1016/j.mib.2025.102637

Sophia A Adler , Grayson L Chadwick , Dipti D Nayak

引用次数: 0

Brownian ratchet mechanisms for carboxysome positioning in bacteria 细菌中羧基体定位的布朗棘轮机制

IF 7.5 2区生物学

Current opinion in microbiology Pub Date : 2025-07-29 DOI: 10.1016/j.mib.2025.102638

Christopher A Azaldegui , Anthony G Vecchiarelli , Julie S Biteen

引用次数: 0