Microbiological research最新文献_第2页

Longitudinal multi-omics pilot study: Small sample size human model of gut microbiota-mitochondrial metabolic dysregulation in primary biliary cholangitis 纵向多组学先导研究：原发性胆道胆管炎中肠道微生物-线粒体代谢失调的小样本人体模型。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-03 DOI: 10.1016/j.micres.2026.128465

Jing Lou , Xiaoxiang Hu , Ren Yan , Jiamin Duan , Bingbing Du , Feiyu Wang , Yini Shao , Huiyong Jiang , Lanjuan Li , Longxian Lv

Ursodeoxycholic acid (UDCA) is the first-line therapy for primary biliary cholangitis (PBC), yet a subset of patients responds inadequately, with the underlying mechanisms remaining unclear. In this longitudinal, multi-omics pilot study employing a small-sample human model, we investigated the role of gut microbiota-mitochondrial metabolic dysregulation in influencing the heterogeneity of UDCA treatment response. Our exploratory analysis revealed that UDCA nonresponders exhibit persistent gut dysbiosis, characterized by the depletion of beneficial butyrate-producing bacteria, the expansion of opportunistic fungi such as Candida albicans, and the enrichment of a pro-inflammatory bacterial network centered on Collinsella. Functionally, this dysbiosis in nonresponders is characterized by an enrichment of microbial virulence factors (e.g., flagella) and impaired host energy metabolism, particularly mitochondrial tricarboxylic acid (TCA) cycle dysfunction, as supported by persistently elevated serum pyruvate levels. Conversely, UDCA responders exhibit remodeling of the gut microbiota and improved mitochondrial function, with significant enrichment of serum itaconate. As a proof-of-concept, an integrated microbiota-metabolite predictive model showed potential in identifying nonresponders within our cohort.However, its performance requires validation in independent cohorts, and its clinical utility remains unknown. Overall, this pilot study proposes that UDCA nonresponse may represent a distinct pathological state centered on persistent mitochondrial metabolic dysfunction, offering preliminary insights for developing personalized therapeutic strategies that target the gut-mitochondrion axis.

熊去氧胆酸（UDCA）是原发性胆道胆管炎（PBC）的一线治疗药物，但有一部分患者反应不充分，其潜在机制尚不清楚。在这项采用小样本人体模型的纵向多组学先导研究中，我们研究了肠道微生物-线粒体代谢失调在影响UDCA治疗反应异质性中的作用。我们的探索性分析显示，UDCA无应答者表现出持续的肠道生态失调，其特征是有益的丁酸产生细菌的消耗，白色念珠菌等机会性真菌的扩张，以及以Collinsella为中心的促炎细菌网络的富集。功能上，无应答者的这种生态失调的特点是微生物毒力因子（如鞭毛）的富集和宿主能量代谢受损，特别是线粒体三羧酸（TCA）循环功能障碍，这与持续升高的血清丙酮酸水平有关。相反，UDCA应答者表现出肠道微生物群的重塑和线粒体功能的改善，血清衣康酸显著富集。作为概念验证，综合微生物群代谢物预测模型显示出在我们的队列中识别无反应的潜力。然而，它的性能需要在独立的队列验证，其临床应用仍然未知。总的来说，这项初步研究表明，UDCA无反应可能代表了一种以持续线粒体代谢功能障碍为中心的独特病理状态，为开发针对肠道-线粒体轴的个性化治疗策略提供了初步见解。

{"title":"Longitudinal multi-omics pilot study: Small sample size human model of gut microbiota-mitochondrial metabolic dysregulation in primary biliary cholangitis","authors":"Jing Lou , Xiaoxiang Hu , Ren Yan , Jiamin Duan , Bingbing Du , Feiyu Wang , Yini Shao , Huiyong Jiang , Lanjuan Li , Longxian Lv","doi":"10.1016/j.micres.2026.128465","DOIUrl":"10.1016/j.micres.2026.128465","url":null,"abstract":"<div><div>Ursodeoxycholic acid (UDCA) is the first-line therapy for primary biliary cholangitis (PBC), yet a subset of patients responds inadequately, with the underlying mechanisms remaining unclear. In this longitudinal, multi-omics pilot study employing a small-sample human model, we investigated the role of gut microbiota-mitochondrial metabolic dysregulation in influencing the heterogeneity of UDCA treatment response. Our exploratory analysis revealed that UDCA nonresponders exhibit persistent gut dysbiosis, characterized by the depletion of beneficial butyrate-producing bacteria, the expansion of opportunistic fungi such as <em>Candida albicans</em>, and the enrichment of a pro-inflammatory bacterial network centered on <em>Collinsella</em>. Functionally, this dysbiosis in nonresponders is characterized by an enrichment of microbial virulence factors (e.g., flagella) and impaired host energy metabolism, particularly mitochondrial tricarboxylic acid (TCA) cycle dysfunction, as supported by persistently elevated serum pyruvate levels. Conversely, UDCA responders exhibit remodeling of the gut microbiota and improved mitochondrial function, with significant enrichment of serum itaconate. As a proof-of-concept, an integrated microbiota-metabolite predictive model showed potential in identifying nonresponders within our cohort.However, its performance requires validation in independent cohorts, and its clinical utility remains unknown. Overall, this pilot study proposes that UDCA nonresponse may represent a distinct pathological state centered on persistent mitochondrial metabolic dysfunction, offering preliminary insights for developing personalized therapeutic strategies that target the gut-mitochondrion axis.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128465"},"PeriodicalIF":6.9,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Morphological classification of Schizochytrium and mutagenic selection of high-oil-producing strains based on deep learning 裂壶菌形态分类及基于深度学习的高产菌株诱变选择。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-03 DOI: 10.1016/j.micres.2026.128464

Yu Qin , Ying Ou , Jian Zheng , Shoushuai Feng , Li Xie , Qiong Wang , Hailing Li , Ren Gong , Hailin Yang

As a natural producer of omega-3 fatty acids, Schizochytrium demonstrates exceptional cell density and docosahexaenoic acid (DHA) production efficiency, establishing its status as a microbial platform of industrial significance. However, the absence of real-time fermentation monitoring systems constrains production optimization and hinders the sustainable commercialization of omega-3 products. Morphometric analysis offers potential for tracking microbial growth and metabolite accumulation, yet the complex relationships between Schizochytrium morphology, biomass dynamics, and lipid biosynthesis remain unresolved. Conventional morphological characterization relies on labor-intensive microscopic observation by trained personnel, necessitating automated image analysis solutions. We developed a novel 13-class morphotype classification system integrating cellular division characteristics and lipid droplet parameters, coupled with a purpose-built object detection architecture. The enhanced MLC-YOLO framework achieved 84.2 % mean average precision (mAP), representing a 2.2 % improvement over the standard YOLOv8s implementation. Fermentation monitoring identified strong positive correlations (p < 0.001) between Lipid-saturated unicells (G11) and lipid yield, whereas Small lipid droplet tripartite cells (G4) and Small lipid droplet quadripartite cells (G6) inversely correlated with productivity. Application of the G11/(G4 +G6) selection index facilitated the isolation of mutant strain S62, which had a lipid content of 50.46 %, an increase of 1.96 % over the parental strain. This study addresses fundamental knowledge gaps in Schizochytrium morphology, establishes deep learning-enabled cellular phenotyping as a viable strain selection strategy, and propels the development of smart biomanufacturing systems for industrial omega-3 production.

Schizochytrium是omega-3脂肪酸的天然生产者，具有卓越的细胞密度和二十二碳六烯酸（DHA）的生产效率，确立了其作为具有工业意义的微生物平台的地位。然而，缺乏实时发酵监测系统限制了生产优化，阻碍了omega-3产品的可持续商业化。形态计量学分析为追踪微生物生长和代谢物积累提供了潜力，但裂体形态、生物量动态和脂质生物合成之间的复杂关系仍未得到解决。传统的形态表征依赖于训练有素的人员的劳动密集型显微镜观察，需要自动化图像分析解决方案。我们开发了一种新的13类形态分类系统，结合细胞分裂特征和脂滴参数，以及专用的目标检测架构。增强的MLC-YOLO框架实现了84.2 %的平均精度（mAP），比标准的YOLOv8s实现提高了2.2 %。发酵监测发现了很强的正相关性(p

{"title":"Morphological classification of Schizochytrium and mutagenic selection of high-oil-producing strains based on deep learning","authors":"Yu Qin , Ying Ou , Jian Zheng , Shoushuai Feng , Li Xie , Qiong Wang , Hailing Li , Ren Gong , Hailin Yang","doi":"10.1016/j.micres.2026.128464","DOIUrl":"10.1016/j.micres.2026.128464","url":null,"abstract":"<div><div>As a natural producer of omega-3 fatty acids, <em>Schizochytrium</em> demonstrates exceptional cell density and docosahexaenoic acid (DHA) production efficiency, establishing its status as a microbial platform of industrial significance. However, the absence of real-time fermentation monitoring systems constrains production optimization and hinders the sustainable commercialization of omega-3 products. Morphometric analysis offers potential for tracking microbial growth and metabolite accumulation, yet the complex relationships between <em>Schizochytrium</em> morphology, biomass dynamics, and lipid biosynthesis remain unresolved. Conventional morphological characterization relies on labor-intensive microscopic observation by trained personnel, necessitating automated image analysis solutions. We developed a novel 13-class morphotype classification system integrating cellular division characteristics and lipid droplet parameters, coupled with a purpose-built object detection architecture. The enhanced MLC-YOLO framework achieved 84.2 % mean average precision (mAP), representing a 2.2 % improvement over the standard YOLOv8s implementation. Fermentation monitoring identified strong positive correlations (<em>p</em> < 0.001) between Lipid-saturated unicells (G11) and lipid yield, whereas Small lipid droplet tripartite cells (G4) and Small lipid droplet quadripartite cells (G6) inversely correlated with productivity. Application of the G11/(G4 +G6) selection index facilitated the isolation of mutant strain S62, which had a lipid content of 50.46 %, an increase of 1.96 % over the parental strain. This study addresses fundamental knowledge gaps in <em>Schizochytrium</em> morphology, establishes deep learning-enabled cellular phenotyping as a viable strain selection strategy, and propels the development of smart biomanufacturing systems for industrial omega-3 production.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128464"},"PeriodicalIF":6.9,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

The molecular arms race: Xenophagy, pathogen evasion, and emerging host-directed therapies 分子军备竞赛：异种噬，病原体逃避，和新兴的宿主导向疗法。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-02-01 DOI: 10.1016/j.micres.2026.128460

Onaiza Ansari , Farhan Ahmed , Nilofar Siddiquee , Anam Mursaleen , Syeda Rushna , Javaid Ahmad Sheikh , Mohd Shariq

Xenophagy, a form of selective autophagy targeting intracellular pathogens, constitutes a central arm of cell-autonomous innate immunity. This review synthesizes recent advances in the molecular regulation of xenophagy, emphasizing ubiquitin-dependent and ubiquitin-independent cargo tagging, receptor redundancy and context dependence, and post-translational control of autophagy-related 8/microtubule-associated protein 1 light chain 3 (ATG8/MAP1LC3/LC3) engagement. We discuss how pathogens exploit or evade xenophagic defenses at multiple checkpoints, cargo recognition, receptor recruitment, autophagosome biogenesis, and lysosomal fusion, highlighting mechanistically defined bacterial and viral countermeasures. Attention is given to the distinction between canonical xenophagy and non-canonical LC3-associated phagocytosis (LAP), clarifying their divergent regulatory logic and functional outcomes. We further examine the integration of xenophagy with innate immune signaling, antigen processing and presentation, and intercellular communication via exosomes, thereby linking intracellular pathogen restriction to adaptive immunity. Emerging discovery platforms, including multi-omics and clustered regularly interspaced short palindromic repeats (CRISPR-based) genetic screens, are evaluated for their potential to uncover novel xenophagy regulators. Finally, we critically assess translational opportunities for xenophagy-targeted host-directed therapies, emphasizing pathogen-specific context, tissue-restricted delivery, and the risks of non-selective autophagy modulation. Together, this review provides a mechanistic and translational framework for understanding xenophagy as a dynamic, context-dependent immune defense pathway rather than a uniformly protective degradative process.

异体自噬是一种针对细胞内病原体的选择性自噬，是细胞自主先天免疫的重要组成部分。本文综述了近年来异种自噬分子调控的最新进展，重点介绍了自噬相关的8/微管相关蛋白1轻链3 （ATG8/MAP1LC3/LC3）参与的翻译后调控，包括泛素依赖性和非泛素依赖性货标记、受体冗余和上下文依赖性。我们讨论了病原体如何在多个检查点、货物识别、受体招募、自噬体生物发生和溶酶体融合中利用或逃避异食防御，并强调了细菌和病毒对策的机制定义。关注典型异种吞噬和非典型lc3相关吞噬（LAP）之间的区别，阐明它们不同的调节逻辑和功能结果。我们进一步研究了异种吞噬与先天免疫信号、抗原加工和递呈以及通过外泌体的细胞间通讯的整合，从而将细胞内病原体限制与适应性免疫联系起来。新兴的发现平台，包括多组学和集群定期间隔短回文重复（基于crispr的）基因筛选，因其发现新的异种噬调节因子的潜力而受到评估。最后，我们批判性地评估了针对异种自噬的宿主定向疗法的转化机会，强调病原体特异性背景，组织限制性递送以及非选择性自噬调节的风险。总之，这篇综述提供了一个机制和翻译框架来理解异体吞噬是一个动态的、环境依赖的免疫防御途径，而不是一个统一的保护性降解过程。

{"title":"The molecular arms race: Xenophagy, pathogen evasion, and emerging host-directed therapies","authors":"Onaiza Ansari , Farhan Ahmed , Nilofar Siddiquee , Anam Mursaleen , Syeda Rushna , Javaid Ahmad Sheikh , Mohd Shariq","doi":"10.1016/j.micres.2026.128460","DOIUrl":"10.1016/j.micres.2026.128460","url":null,"abstract":"<div><div>Xenophagy, a form of selective autophagy targeting intracellular pathogens, constitutes a central arm of cell-autonomous innate immunity. This review synthesizes recent advances in the molecular regulation of xenophagy, emphasizing ubiquitin-dependent and ubiquitin-independent cargo tagging, receptor redundancy and context dependence, and post-translational control of autophagy-related 8/microtubule-associated protein 1 light chain 3 (ATG8/MAP1LC3/LC3) engagement. We discuss how pathogens exploit or evade xenophagic defenses at multiple checkpoints, cargo recognition, receptor recruitment, autophagosome biogenesis, and lysosomal fusion, highlighting mechanistically defined bacterial and viral countermeasures. Attention is given to the distinction between canonical xenophagy and non-canonical LC3-associated phagocytosis (LAP), clarifying their divergent regulatory logic and functional outcomes. We further examine the integration of xenophagy with innate immune signaling, antigen processing and presentation, and intercellular communication via exosomes, thereby linking intracellular pathogen restriction to adaptive immunity. Emerging discovery platforms, including multi-omics and clustered regularly interspaced short palindromic repeats (CRISPR-based) genetic screens, are evaluated for their potential to uncover novel xenophagy regulators. Finally, we critically assess translational opportunities for xenophagy-targeted host-directed therapies, emphasizing pathogen-specific context, tissue-restricted delivery, and the risks of non-selective autophagy modulation. Together, this review provides a mechanistic and translational framework for understanding xenophagy as a dynamic, context-dependent immune defense pathway rather than a uniformly protective degradative process.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128460"},"PeriodicalIF":6.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

The sodium alginate-producing gene algD reduces Pseudomonas putida strain XMS-1-mediated Cd uptake in Lactuca sativa by increasing the relative abundances of Cd stabilization-related bacterial communities and functional genes 海藻酸钠产生基因algD通过增加与Cd稳定相关的细菌群落和功能基因的相对丰度，降低了腐殖酸假单胞菌xms -1介导的油菜Cd吸收。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-31 DOI: 10.1016/j.micres.2026.128463

Yanyan Ge , Fangfang Jiang , Xiaoyu Zhang , Qi Sheng , Linyan He , Xiafang Sheng

In this study, the effects of Pseudomonas putida strain XMS-1 and its sodium alginate (SA)-producing gene algD deletion mutant (∆algD) on cadmium (Cd) immobilization in solution, and Cd availability and uptake in lettuce plants and mechanisms involved in the contaminated soils were investigated. Compared with XMS-1, ∆algD increased the solution Cd concentration by 57 % and reduced the cell surface-adsorbed and intracellular Cd contents by 44–57 % after 36 h of incubation. Compared with XMS-1, ∆algD significantly decreased the lettuce biomass, iron/manganese oxide- and organic matter-bound Cd contents, pH values, and polysaccharide and mineral-associated organic carbon contents and increased the exchange of Cd and lettuce leaf Cd contents in the soils. Furthermore, compared with XMS-1, ∆algD significantly reduced the relative abundances of Cd-immobilizing related abundant (Knoellia, Pseudomonas, Lysobacter, Microbacterium, and Flavisolibacter) and rare (Saccharothrix, Pajaroellobacter, Dyadobacter, Stenotrophomonas, Candidatus Koribacter, and Mumia) genera and functional genes mnxG, cumA, mnp, and epsA involved in manganese oxidation, ferromanganese nodule formation, and exopolysaccharide production in the rhizosphere soils of lettuce plants compared to XMS-1. Correlation analysis revealed negative relationships between the relative abundances of these bacterial populations and Cd uptake in lettuce tissues. These findings suggest the significant effects of algD in XMS-1 on reducing Cd availability and accumulation in lettuce through enriching the Cd-immobilizing related bacterial communities and functional genes in the contaminated soils. Our findings offer new insights into the mechanisms underlying algD-mediated reduction in Cd accumulation in lettuce by XMS-1, laying a crucial foundation for the use of SA-producing bacteria to ensure safe vegetable production in the Cd-contaminated soils.

以腐殖假单胞菌XMS-1及其产藻酸钠基因缺失突变体（∆algD）为研究对象，研究了菌株XMS-1及其产藻酸钠基因缺失突变体（∆algD）对溶液中镉（Cd）的固定化、生菜对Cd的吸收和有效性及其在污染土壤中的作用机制。与XMS-1相比，孵育36 h后，∆algD使溶液Cd浓度提高了57 %，使细胞表面吸附和细胞内Cd含量降低了44-57 %。与XMS-1相比，∆algD显著降低了生菜生物量、铁/锰氧化物和有机质结合型Cd含量、pH值、多糖和矿物相关有机碳含量，增加了土壤中Cd交换和生菜叶片Cd含量。此外，与XMS-1相比，∆algD显著降低了cd固定化相关的丰富（Knoellia、Pseudomonas、Lysobacter、Microbacterium、Flavisolibacter）和稀有（Saccharothrix、Pajaroellobacter、Dyadobacter、Stenotrophomonas、Candidatus Koribacter和Mumia）属和功能基因mnxG、cumA、mnp和epsA的相对丰度，这些基因与锰氧化、锰铁结核形成有关。与XMS-1相比，莴苣植株根际土壤中胞外多糖的产量。相关分析表明，这些细菌群体的相对丰度与生菜组织对Cd的吸收呈负相关。这些结果表明，在XMS-1中添加海藻酸d可以通过丰富污染土壤中Cd固定化相关细菌群落和功能基因来降低生菜Cd的有效性和积累。我们的研究结果为揭示藻类d介导的XMS-1减少生菜Cd积累的机制提供了新的见解，为利用产sa细菌在Cd污染土壤中确保蔬菜安全生产奠定了重要基础。

{"title":"The sodium alginate-producing gene algD reduces Pseudomonas putida strain XMS-1-mediated Cd uptake in Lactuca sativa by increasing the relative abundances of Cd stabilization-related bacterial communities and functional genes","authors":"Yanyan Ge , Fangfang Jiang , Xiaoyu Zhang , Qi Sheng , Linyan He , Xiafang Sheng","doi":"10.1016/j.micres.2026.128463","DOIUrl":"10.1016/j.micres.2026.128463","url":null,"abstract":"<div><div>In this study, the effects of <em>Pseudomonas putida</em> strain XMS-1 and its sodium alginate (SA)-producing gene <em>algD</em> deletion mutant (∆<em>algD</em>) on cadmium (Cd) immobilization in solution, and Cd availability and uptake in lettuce plants and mechanisms involved in the contaminated soils were investigated. Compared with XMS-1, ∆<em>algD</em> increased the solution Cd concentration by 57 % and reduced the cell surface-adsorbed and intracellular Cd contents by 44–57 % after 36 h of incubation. Compared with XMS-1, ∆<em>algD</em> significantly decreased the lettuce biomass, iron/manganese oxide- and organic matter-bound Cd contents, pH values, and polysaccharide and mineral-associated organic carbon contents and increased the exchange of Cd and lettuce leaf Cd contents in the soils. Furthermore, compared with XMS-1, ∆<em>algD</em> significantly reduced the relative abundances of Cd-immobilizing related abundant (<em>Knoellia</em>, <em>Pseudomonas</em>, <em>Lysobacter</em>, <em>Microbacterium</em>, and <em>Flavisolibacter</em>) and rare (<em>Saccharothrix</em>, <em>Pajaroellobacter</em>, <em>Dyadobacter</em>, <em>Stenotrophomonas</em>, <em>Candidatus Koribacter</em>, and <em>Mumia</em>) genera and functional genes <em>mnxG</em>, <em>cumA</em>, <em>mnp</em>, and <em>epsA</em> involved in manganese oxidation, ferromanganese nodule formation, and exopolysaccharide production in the rhizosphere soils of lettuce plants compared to XMS-1. Correlation analysis revealed negative relationships between the relative abundances of these bacterial populations and Cd uptake in lettuce tissues. These findings suggest the significant effects of <em>algD</em> in XMS-1 on reducing Cd availability and accumulation in lettuce through enriching the Cd-immobilizing related bacterial communities and functional genes in the contaminated soils. Our findings offer new insights into the mechanisms underlying <em>algD</em>-mediated reduction in Cd accumulation in lettuce by XMS-1, laying a crucial foundation for the use of SA-producing bacteria to ensure safe vegetable production in the Cd-contaminated soils.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128463"},"PeriodicalIF":6.9,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Functional characterization of a Con7-related transcription factor in Coprinopsis cinerea indicates evolutionary conservation of morphogenetic roles Coprinopsis cinerea中con7相关转录因子的功能表征表明形态发生作用的进化守恒。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-31 DOI: 10.1016/j.micres.2026.128462

Hongli Wu , Zsolt Merényi , Máté Virágh , Xiao-Bin Liu , Botond Hegedüs , Zhihao Hou , Edit Ábrahám , Anett Fürtön , Zsolt Kristóffy , Zoltán Lipinszki , László G. Nagy

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) exhibit the highest degree of multicellular complexity in fungi, yet the molecular underpinnings of their developmental programs remain incompletely understood. Here, we characterize gcd1, a gene encoding a transcription factor in the Con7 subfamily of C2H2-type zinc finger proteins. This subfamily has previously been implicated in pathogenic morphogenesis in Ascomycota, but its role in Agaricomycetes has not previously been addressed. In Coprinopsis cinerea, CRISPR/Cas9-mediated deletion of gcd1 resulted in strains with severely impaired fruiting body morphogenesis, with malformed cap, stipe, and gill tissues. Gcd1 deletion strains lacked universal veil, resembling species with open (gymnocarpous) development. We find that GCD1/Con7 homologs are widely distributed in most Dikarya species and are mostly encoded by a single gene in each species’ genome. Transcriptome analyses identified several misregulated genes in the Δgcd1 mutant, which pinpoint potential mechanisms underlying its developmental defects as well as provided insights into the morphogenesis of mushroom fruiting bodies. These findings establish GCD1 as a key regulator of multicellular development in C. cinerea and broaden the known functions of Con7-like transcription factors to include fruiting body morphogenesis in Agaricomycetes. Overall, our results and the morphogenetic role of Con7-like transcription factors of Ascomycota suggest functional conservation over half a billion years of evolution.

蘑菇形成真菌的子实体在真菌中表现出最高程度的多细胞复杂性，但其发育程序的分子基础仍未完全了解。在这里，我们描述了gcd1，一个编码c2h2型锌指蛋白Con7亚家族转录因子的基因。这个亚家族以前与子囊菌的致病形态发生有关，但它在真菌中的作用以前没有得到解决。在Coprinopsis cinerea中，CRISPR/ cas9介导的gcd1缺失导致菌株的子实体形态发生严重受损，帽、柄和鳃组织畸形。Gcd1缺失菌株缺乏普遍面纱，类似于开放（裸心）发育的物种。我们发现GCD1/Con7同源物在大多数Dikarya物种中广泛分布，并且在每个物种的基因组中大多由单个基因编码。转录组分析在Δgcd1突变体中发现了几个错误调控的基因，这明确了其发育缺陷的潜在机制，并为蘑菇子实体的形态发生提供了见解。这些发现证实了GCD1是C. cinerea多细胞发育的关键调控因子，并将con7样转录因子的已知功能扩展到包括菌丝菌的子实体形态发生。总的来说，我们的研究结果和子囊菌con7样转录因子的形态发生作用表明，在5亿年的进化过程中，子囊菌的功能保持不变。

{"title":"Functional characterization of a Con7-related transcription factor in Coprinopsis cinerea indicates evolutionary conservation of morphogenetic roles","authors":"Hongli Wu , Zsolt Merényi , Máté Virágh , Xiao-Bin Liu , Botond Hegedüs , Zhihao Hou , Edit Ábrahám , Anett Fürtön , Zsolt Kristóffy , Zoltán Lipinszki , László G. Nagy","doi":"10.1016/j.micres.2026.128462","DOIUrl":"10.1016/j.micres.2026.128462","url":null,"abstract":"<div><div>Fruiting bodies of mushroom-forming fungi (Agaricomycetes) exhibit the highest degree of multicellular complexity in fungi, yet the molecular underpinnings of their developmental programs remain incompletely understood. Here, we characterize <em>gcd1</em>, a gene encoding a transcription factor in the Con7 subfamily of C2H2-type zinc finger proteins. This subfamily has previously been implicated in pathogenic morphogenesis in Ascomycota, but its role in Agaricomycetes has not previously been addressed. In <em>Coprinopsis cinerea</em>, CRISPR/Cas9-mediated deletion of <em>gcd1</em> resulted in strains with severely impaired fruiting body morphogenesis, with malformed cap, stipe, and gill tissues. <em>Gcd1</em> deletion strains lacked universal veil, resembling species with open (gymnocarpous) development. We find that GCD1/Con7 homologs are widely distributed in most Dikarya species and are mostly encoded by a single gene in each species’ genome. Transcriptome analyses identified several misregulated genes in the Δ<em>gcd1</em> mutant, which pinpoint potential mechanisms underlying its developmental defects as well as provided insights into the morphogenesis of mushroom fruiting bodies. These findings establish GCD1 as a key regulator of multicellular development in <em>C. cinerea</em> and broaden the known functions of Con7-like transcription factors to include fruiting body morphogenesis in Agaricomycetes. Overall, our results and the morphogenetic role of Con7-like transcription factors of Ascomycota suggest functional conservation over half a billion years of evolution.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128462"},"PeriodicalIF":6.9,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Lactiplantibacillus plantarum BGI-N6 mitigates obesity-linked inflammation and oxidative stress via gut microbiota-mediated metabolites 植物乳杆菌BGI-N6通过肠道微生物介导的代谢物减轻与肥胖相关的炎症和氧化应激。

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-30 DOI: 10.1016/j.micres.2026.128461

Hui Guo , Wanjie Zhang , Dongwei Zhang , Xiaojie Li , Yan Qin Tan

Obesity-driven systemic inflammation is a critical contributor in the progression of metabolic diseases. While lactic acid bacteria (LAB) are recognized for countering diet-induced obesity, their specific role in mitigating the associated inflammatory pathways requires further elucidation. This study investigated the capacity of a novel LAB strain, Lactiplantibacillus plantarum BGI-N6 (N6), to alleviate obesity and its related inflammatory responses in a high-fat diet (HFD)-fed Sprague-Dawley (SD) rat model. N6 supplementation effectively attenuated body weight gain, fat deposition, and liver steatosis, while concurrently improving systemic metrics such as blood lipid profiles. Crucially, the treatment significantly reduced HFD-induced systemic inflammation and oxidative stress. Analysis of the gut microbiota demonstrated that N6 administration modulated gut microbiota composition, enhancing β-diversity and reducing the abundance of pro-inflammatory taxa, including Sutterella wadsworthensis, Bilophila wadsworthia, and Holdemania filiformis. These structural changes were accompanied by metabolic shifts, specifically an increased production of butyric and valeric acids and a decrease in propionic acid. Furthermore, N6 specifically downregulated bacterial biosynthesis pathways for lipopolysaccharide (LPS), an effect attributed to the reduced abundance of key gram-negative species such as Sutterella wadsworthensis, resulting in significantly lower serum LPS levels. Correlation analyses confirmed the strong association of these microbial and metabolic changes with improved metabolic and inflammatory parameters. Collectively, these findings demonstrate that N6 ameliorates obesity-induced inflammation and oxidative stress through a multi-faceted mechanism involving gut microbiota restructuring, SCFA modulation, and LPS reduction, underscoring its potential as a therapeutic probiotic for metabolic disorders.

肥胖引起的全身性炎症是代谢性疾病进展的关键因素。虽然乳酸菌（LAB）被认为可以对抗饮食引起的肥胖，但它们在减轻相关炎症途径中的具体作用还需要进一步阐明。本研究研究了一种新型乳酸菌植物乳杆菌BGI-N6 （N6）在高脂肪饮食（HFD）喂养的Sprague-Dawley （SD）大鼠模型中减轻肥胖及其相关炎症反应的能力。补充N6有效地减轻了体重增加、脂肪沉积和肝脏脂肪变性，同时改善了血脂等系统指标。至关重要的是，治疗显著降低了hfd诱导的全身炎症和氧化应激。肠道菌群分析表明，N6调节了肠道菌群组成，增强了β-多样性，减少了促炎类群的丰度，包括wadsworthensis Sutterella wadsworthia、Bilophila wadsworthia和Holdemania filiformis。这些结构变化伴随着代谢变化，特别是丁酸和戊酸的增加和丙酸的减少。此外，N6特异性下调细菌脂多糖（LPS）的生物合成途径，这一作用归因于关键革兰氏阴性菌（如wadsworthsutterella）的丰度降低，导致血清LPS水平显著降低。相关分析证实，这些微生物和代谢变化与代谢和炎症参数的改善密切相关。总之，这些研究结果表明，N6通过肠道菌群重组、SCFA调节和LPS减少等多方面机制改善肥胖诱导的炎症和氧化应激，强调了其作为代谢紊乱治疗益生菌的潜力。

{"title":"Lactiplantibacillus plantarum BGI-N6 mitigates obesity-linked inflammation and oxidative stress via gut microbiota-mediated metabolites","authors":"Hui Guo , Wanjie Zhang , Dongwei Zhang , Xiaojie Li , Yan Qin Tan","doi":"10.1016/j.micres.2026.128461","DOIUrl":"10.1016/j.micres.2026.128461","url":null,"abstract":"<div><div>Obesity-driven systemic inflammation is a critical contributor in the progression of metabolic diseases. While lactic acid bacteria (LAB) are recognized for countering diet-induced obesity, their specific role in mitigating the associated inflammatory pathways requires further elucidation. This study investigated the capacity of a novel LAB strain, <em>Lactiplantibacillus plantarum</em> BGI-N6 (N6), to alleviate obesity and its related inflammatory responses in a high-fat diet (HFD)-fed Sprague-Dawley (SD) rat model. N6 supplementation effectively attenuated body weight gain, fat deposition, and liver steatosis, while concurrently improving systemic metrics such as blood lipid profiles. Crucially, the treatment significantly reduced HFD-induced systemic inflammation and oxidative stress. Analysis of the gut microbiota demonstrated that N6 administration modulated gut microbiota composition, enhancing β-diversity and reducing the abundance of pro-inflammatory taxa, including <em>Sutterella wadsworthensis</em>, <em>Bilophila wadsworthia</em>, and <em>Holdemania filiformis</em>. These structural changes were accompanied by metabolic shifts, specifically an increased production of butyric and valeric acids and a decrease in propionic acid. Furthermore, N6 specifically downregulated bacterial biosynthesis pathways for lipopolysaccharide (LPS), an effect attributed to the reduced abundance of key gram-negative species such as <em>Sutterella wadsworthensis</em>, resulting in significantly lower serum LPS levels. Correlation analyses confirmed the strong association of these microbial and metabolic changes with improved metabolic and inflammatory parameters. Collectively, these findings demonstrate that N6 ameliorates obesity-induced inflammation and oxidative stress through a multi-faceted mechanism involving gut microbiota restructuring, SCFA modulation, and LPS reduction, underscoring its potential as a therapeutic probiotic for metabolic disorders.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128461"},"PeriodicalIF":6.9,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Copper gluconate drives adherent-invasive Escherichia coli LF82 into a viable-but-non-culturable state: Mechanisms of persistence and susceptibility 葡萄糖酸铜驱动黏附侵袭性大肠杆菌LF82进入存活但不可培养的状态：持久性和易感性的机制

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-29 DOI: 10.1016/j.micres.2026.128457

Zinuo An, Liangbin Hu, Lili Zhao, Wensheng Liang, Hongbo Li, Tian Lu, Haizhen Mo, Liping Liu

Adherent-invasive Escherichia coli (AIEC) LF82 is closely linked to Crohn’s disease and can persist within macrophages in a quiescent, growth-arrested state. Here, we show that cupric gluconate (Cu Glu) promoted cell death in E. coli MG1655, yet drove E. coli LF82 into a viable-but-non-culturable (VBNC) state. VBNC induction was time dependent and modulated by temperature. VBNC cells remained susceptible to ampicillin and tetracycline but were tolerant to ciprofloxacin. To probe whether capsule-associated factors contribute to the strain-dependent outcome, we heterologously expressed kpsM, kpsT, or kpsMT in MG1655. This increased MG1655 tolerance to Cu Glu but did not induce a VBNC phenotype. Cu Glu increased intracellular Cu⁺ and ROS in LF82 without detectable lipid peroxidation or DNA damage. Copper or ferrous-iron chelation prevented VBNC entry and rescued cells otherwise destined to die, whereas redox modulators shifted VBNC outcomes. Glutathione and catalase resuscitated a small subset, implicating H₂O₂-driven oxidative stress in VBNC fate. Proteomics revealed repression of energy metabolism together with enhanced outer-membrane maintenance and Fe-S cluster repair. Notably, ascorbic acid (Vc) abolished resuscitation and rapidly killed VBNC cells by promoting labile Fe²⁺ release and, together with Cu⁺, amplifying Fenton chemistry to damage membranes without a lipid-peroxidation signature. These findings define a copper-dependent VBNC program in LF82 and provide mechanistic insight into how metal redox imbalance and oxidative stress shape VBNC maintenance and clearance.

粘附-侵袭性大肠杆菌（AIEC） LF82与克罗恩病密切相关，可以在巨噬细胞中以静止、生长停止的状态持续存在。在这里，我们发现葡萄糖酸铜（Cu Glu）促进了大肠杆菌MG1655的细胞死亡，而使大肠杆菌LF82进入可存活但不可培养（VBNC）状态。VBNC的诱导是时间依赖性的，并受温度调节。VBNC细胞对氨苄西林和四环素敏感，但对环丙沙星耐受。为了探究胶囊相关因素是否与菌株依赖的结果有关，我们在MG1655中异种表达了kpsM、kpsT或kpsMT。这增加了MG1655对Cu - Glu的耐受性，但没有诱导VBNC表型。Cu Glu增加了LF82细胞内Cu+和ROS，但没有检测到脂质过氧化或DNA损伤。铜或铁铁螯合阻止了VBNC的进入，挽救了注定死亡的细胞，而氧化还原调节剂改变了VBNC的结果。谷胱甘肽和过氧化氢酶复苏了一小部分，暗示h2o2驱动的氧化应激在VBNC命运中。蛋白质组学显示能量代谢受到抑制，外膜维持和Fe-S簇修复增强。值得注意的是，抗坏血酸（Vc）通过促进不稳定的Fe2+释放，并与Cu+一起，放大Fenton化学，破坏膜，而不具有脂质过氧化特征，从而终止复苏并迅速杀死VBNC细胞。这些发现定义了LF82中铜依赖的VBNC程序，并提供了金属氧化还原失衡和氧化应激如何影响VBNC维持和清除的机制见解。

{"title":"Copper gluconate drives adherent-invasive Escherichia coli LF82 into a viable-but-non-culturable state: Mechanisms of persistence and susceptibility","authors":"Zinuo An, Liangbin Hu, Lili Zhao, Wensheng Liang, Hongbo Li, Tian Lu, Haizhen Mo, Liping Liu","doi":"10.1016/j.micres.2026.128457","DOIUrl":"10.1016/j.micres.2026.128457","url":null,"abstract":"<div><div>Adherent-invasive <em>Escherichia coli</em> (AIEC) LF82 is closely linked to Crohn’s disease and can persist within macrophages in a quiescent, growth-arrested state. Here, we show that cupric gluconate (Cu Glu) promoted cell death in <em>E. coli</em> MG1655, yet drove <em>E. coli</em> LF82 into a viable-but-non-culturable (VBNC) state. VBNC induction was time dependent and modulated by temperature. VBNC cells remained susceptible to ampicillin and tetracycline but were tolerant to ciprofloxacin. To probe whether capsule-associated factors contribute to the strain-dependent outcome, we heterologously expressed <em>kpsM</em>, <em>kpsT</em>, or <em>kpsMT</em> in MG1655. This increased MG1655 tolerance to Cu Glu but did not induce a VBNC phenotype. Cu Glu increased intracellular Cu<sup>+</sup> and ROS in LF82 without detectable lipid peroxidation or DNA damage. Copper or ferrous-iron chelation prevented VBNC entry and rescued cells otherwise destined to die, whereas redox modulators shifted VBNC outcomes. Glutathione and catalase resuscitated a small subset, implicating H<sub>2</sub>O<sub>2</sub>-driven oxidative stress in VBNC fate. Proteomics revealed repression of energy metabolism together with enhanced outer-membrane maintenance and Fe-S cluster repair. Notably, ascorbic acid (Vc) abolished resuscitation and rapidly killed VBNC cells by promoting labile Fe<sup>2+</sup> release and, together with Cu<sup>+</sup>, amplifying Fenton chemistry to damage membranes without a lipid-peroxidation signature. These findings define a copper-dependent VBNC program in LF82 and provide mechanistic insight into how metal redox imbalance and oxidative stress shape VBNC maintenance and clearance.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128457"},"PeriodicalIF":6.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Evolution of phage tail fiber proteins to counter bacterial resistance and improve biocontrol efficacy in plant disease models 植物病害模型中噬菌体尾部纤维蛋白对抗细菌抗性和提高生物防治效果的进化

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-29 DOI: 10.1016/j.micres.2026.128459

Xinyan Xu , Xuefang Huang , Luokai Wang , Jingxian Yang , Munazza Ijaz , Jianping Chen , Kotaro Kiga , Bin Li

Phage therapy is being used to combat pathogenic bacterial infections that threaten plant, animal, and human health. However, its application remains limited by high host specificity and the emergence of bacterial resistance. In this study, we addressed the key issues in phage therapy using rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) strain N1 and its lytic phage NP1. Strain N1 acquired resistance to the phage NP1 through mutations and downregulation of lipopolysaccharide (LPS) biosynthesis genes. A directed evolution assay using phage NP1 and the resistant strain N1R resulted in the development of phage E12–2, which overcame bacterial resistance, expanded its host range and improved bacterial suppression by targeting alternative LPS binding sites. Moreover, genome analysis identified two amino acid substitutions (V303L and G317V) in its tail fiber protein. Additionally, phage E12–2 improved disease control efficiency by 51 % compared to the wild-type phage NP1 and induced plant immunity in a plant disease model. These findings enhance our understanding of how bacteria-phage evolution shapes the dynamics of phage therapy in plants.

噬菌体疗法正被用于对抗威胁植物、动物和人类健康的致病性细菌感染。然而，它的应用仍然受到高宿主特异性和细菌耐药性的限制。在这项研究中，我们讨论了水稻白叶枯病菌（Xanthomonas oryzae pv）噬菌体治疗的关键问题。oryzae （Xoo）菌株N1及其裂解噬菌体NP1。菌株N1通过脂多糖（LPS）生物合成基因的突变和下调获得了对噬菌体NP1的抗性。利用噬菌体NP1和耐药菌株N1R进行定向进化实验，发现噬菌体E12-2克服了细菌耐药性，扩大了其宿主范围，并通过靶向其他LPS结合位点提高了细菌抑制能力。此外，基因组分析发现其尾纤维蛋白中有两个氨基酸替换（V303L和G317V）。此外，与野生型噬菌体NP1相比，噬菌体E12-2提高了51 %的疾病控制效率，并在植物疾病模型中诱导了植物免疫。这些发现增强了我们对噬菌体进化如何影响植物中噬菌体治疗动力学的理解。

{"title":"Evolution of phage tail fiber proteins to counter bacterial resistance and improve biocontrol efficacy in plant disease models","authors":"Xinyan Xu , Xuefang Huang , Luokai Wang , Jingxian Yang , Munazza Ijaz , Jianping Chen , Kotaro Kiga , Bin Li","doi":"10.1016/j.micres.2026.128459","DOIUrl":"10.1016/j.micres.2026.128459","url":null,"abstract":"<div><div>Phage therapy is being used to combat pathogenic bacterial infections that threaten plant, animal, and human health. However, its application remains limited by high host specificity and the emergence of bacterial resistance. In this study, we addressed the key issues in phage therapy using rice bacterial blight pathogen <em>Xanthomonas oryzae</em> pv<em>. oryzae</em> (<em>Xoo</em>) strain N1 and its lytic phage NP1. Strain N1 acquired resistance to the phage NP1 through mutations and downregulation of lipopolysaccharide (LPS) biosynthesis genes. A directed evolution assay using phage NP1 and the resistant strain N1R resulted in the development of phage E12–2, which overcame bacterial resistance, expanded its host range and improved bacterial suppression by targeting alternative LPS binding sites. Moreover, genome analysis identified two amino acid substitutions (V303L and G317V) in its tail fiber protein. Additionally, phage E12–2 improved disease control efficiency by 51 % compared to the wild-type phage NP1 and induced plant immunity in a plant disease model. These findings enhance our understanding of how bacteria-phage evolution shapes the dynamics of phage therapy in plants.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128459"},"PeriodicalIF":6.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Microbial diversity loss affects old and modern barley cultivars differently under varying nitrogen sources 在不同氮源条件下，微生物多样性丧失对老大麦和现代大麦品种的影响不同

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-24 DOI: 10.1016/j.micres.2026.128458

Nikolaj L. Kindtler , Sanea Sheikh , Rujia He , Rute R.da Fonseca , Kristian H. Laursen , Flemming Ekelund

Soil microbial diversity is crucial for plant nutrition and health, yet how its loss affects plant performance remains unclear. We used a dilution-to-extinction approach to test how declining rhizo-microbiome diversity influences two barley cultivars: the modern RGT Planet and the older Babushka. Plants were grown in sterilized systems amended with mineral or organic nitrogen and inoculated with microbiome treatments (10^-¹, 10^-³, 10^-⁵, and 10^-⁷ dilutions), plus a no-inoculum treatment. We used amplicon sequencing (16S, ITS, 18S) to profile rhizosphere communities, and quantified plant biomass, shoot nitrogen, and chitin mineralization. Protists and fungi were present in 10^-¹ and 10^-³ but absent in all others. Microbiome inoculum and nitrogen source explained most variation in rhizo-microbiome composition, with cultivar having a smaller effect. Under organic nitrogen, Babushka showed a marked decline in biomass with decreasing diversity, whereas RGT was largely unaffected, indicating that the older cultivar relied more on a diverse microbiome to maintain growth. At intermediate diversity, when protists and fungi were lost, both cultivars showed improved growth and shoot nitrogen, coinciding with shifts in bacterial composition and loss of potential pathogens. Hence, reduced diversity did not always impair growth, suggesting functional compensation. Under mineral nitrogen, both cultivars were less sensitive to diversity loss. Overall, nitrogen source and cultivar identity modulated plant responses to microbial diversity loss. Diverse microbiomes promoted efficient use of organic nitrogen, particularly for the older cultivar, while the modern cultivar maintained growth at lower diversity. Our results demonstrate that the consequences of diversity loss are context-dependent and cultivar-specific.

土壤微生物多样性对植物营养和健康至关重要，但其损失如何影响植物性能尚不清楚。我们使用稀释到灭绝的方法来测试下降的根茎微生物组多样性如何影响两个大麦品种：现代RGT Planet和较老的Babushka。植物生长在用无机氮或有机氮修饰的无菌系统中，并接种微生物组处理（10-¹、10-³、10- 5和10-⁷稀释度），外加无接种处理。我们使用扩增子测序（16S， ITS, 18S）来分析根际群落，并量化植物生物量，地上部氮和几丁质矿化。原生生物和真菌在10-¹ 和10-³ 中存在，但在其他所有地方都不存在。微生物组接种量和氮源对根际微生物组组成的影响最大，品种对根际微生物组组成的影响较小。在有机氮处理下，随着多样性的降低，巴布什卡的生物量显著下降，而RGT基本未受影响，说明老品种更多地依赖于多样化的微生物组来维持生长。在中等多样性时，当原生生物和真菌消失时，两个品种都表现出生长和发氮的改善，这与细菌组成的变化和潜在病原体的丧失相一致。因此，多样性的减少并不总是损害生长，这表明功能补偿。在矿质氮处理下，两个品种对多样性丧失的敏感性较低。总体而言，氮源和品种特性调节了植物对微生物多样性丧失的响应。微生物组的多样性促进了有机氮的有效利用，特别是对老品种，而现代品种在较低的多样性下保持了生长。我们的研究结果表明，多样性丧失的后果是环境依赖和品种特异性的。

{"title":"Microbial diversity loss affects old and modern barley cultivars differently under varying nitrogen sources","authors":"Nikolaj L. Kindtler , Sanea Sheikh , Rujia He , Rute R.da Fonseca , Kristian H. Laursen , Flemming Ekelund","doi":"10.1016/j.micres.2026.128458","DOIUrl":"10.1016/j.micres.2026.128458","url":null,"abstract":"<div><div>Soil microbial diversity is crucial for plant nutrition and health, yet how its loss affects plant performance remains unclear. We used a dilution-to-extinction approach to test how declining rhizo-microbiome diversity influences two barley cultivars: the modern RGT Planet and the older Babushka. Plants were grown in sterilized systems amended with mineral or organic nitrogen and inoculated with microbiome treatments (10<sup>-</sup>¹, 10<sup>-</sup>³, 10<sup>-</sup>⁵, and 10<sup>-</sup>⁷ dilutions), plus a no-inoculum treatment. We used amplicon sequencing (16S, ITS, 18S) to profile rhizosphere communities, and quantified plant biomass, shoot nitrogen, and chitin mineralization. Protists and fungi were present in 10<sup>-</sup>¹ and 10<sup>-</sup>³ but absent in all others. Microbiome inoculum and nitrogen source explained most variation in rhizo-microbiome composition, with cultivar having a smaller effect. Under organic nitrogen, Babushka showed a marked decline in biomass with decreasing diversity, whereas RGT was largely unaffected, indicating that the older cultivar relied more on a diverse microbiome to maintain growth. At intermediate diversity, when protists and fungi were lost, both cultivars showed improved growth and shoot nitrogen, coinciding with shifts in bacterial composition and loss of potential pathogens. Hence, reduced diversity did not always impair growth, suggesting functional compensation. Under mineral nitrogen, both cultivars were less sensitive to diversity loss. Overall, nitrogen source and cultivar identity modulated plant responses to microbial diversity loss. Diverse microbiomes promoted efficient use of organic nitrogen, particularly for the older cultivar, while the modern cultivar maintained growth at lower diversity. Our results demonstrate that the consequences of diversity loss are context-dependent and cultivar-specific.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128458"},"PeriodicalIF":6.9,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

The contribution of root border cells as a defense barrier against soil-borne pathogen Verticillium dahliae: Insights from the host cotton and the non-host corn 根缘细胞对土壤病原菌大丽花黄萎病的防御屏障的贡献：来自寄主棉花和非寄主玉米的见解

IF 6.9 1区生物学 Q1 MICROBIOLOGY

Microbiological research

Pub Date : 2026-01-23 DOI: 10.1016/j.micres.2026.128452

Sen Zhang , Xiaoyu Wang , Dan Zhang , Ruichi Hua, Yijin Yan, Juan Yang, Jinhu Ma, Jie Wang, Xiaohuan Yang

Verticillium wilt can be caused by the soil-borne fungal pathogen Verticillium dahliae (V. dahliae). It is a destructive vascular pathogen that infects more than 200 plant species, including economically important crops such as cotton. The disease induces severe symptoms such as wilting, chlorosis, and necrosis, ultimately resulting in substantial yield losses. Conventional management strategies, including chemical fungicides and crop rotation, have exhibited limited effectiveness against V. dahliae, emphasizing the urgent need to elucidate innate plant resistance mechanisms for breeding Verticillium-resistant varieties. In this study, the defense mechanisms of root border cells (RBCs) against V. dahliae were investigated. Fluorescence microscopy and cryo-scanning electron microscopy demonstrated that RBCs were viable and free cells, exhibiting round, intermediate, and elongated morphologies. In vitro co-culture assays revealed that viable RBCs isolated from cotton or corn markedly suppressed the growth of V. dahliae, whereas heat-inactivated RBCs lost this antifungal capacity, confirming that the defense mechanism was viability-dependent. Further analysis indicated that under V. dahliae stress, RBCs secreted a thickened mucilage layer enriched in pectin and extracellular DNA (exDNA), which encapsulated fungal hyphae and formed a physical barrier. Metabolomic profiling of RBC secretions from both cotton and corn identified a conserved set of metabolites, including compounds involved in flavone and flavonol biosynthesis, valine, leucine, and isoleucine metabolism, and phenylpropanoid biosynthesis, which could contribute to chemical defense against pathogens. These findings demonstrate the cellular and molecular mechanisms underlying RBC-mediated inhibition of V. dahliae infection and provide insights for developing Verticillium wilt resistance breeding strategies in cotton.

黄萎病可由土壤传播的真菌病原菌大丽花黄萎病（vdahliae）引起。它是一种破坏性的维管病原体，感染200多种植物，包括经济上重要的作物，如棉花。该病引起严重的症状，如萎蔫、黄化和坏死，最终导致大量产量损失。传统的管理策略，包括化学杀菌剂和作物轮作，对大丽花弧菌的有效性有限，因此迫切需要阐明植物的先天抗性机制，以培育抗黄萎病的品种。本研究探讨了根缘细胞对大丽花的防御机制。荧光显微镜和冷冻扫描电镜显示红细胞是有活力的游离细胞，表现出圆形、中间和细长的形态。体外共培养实验表明，从棉花或玉米中分离的活红细胞明显抑制大丽花弧菌的生长，而热灭活红细胞则失去了这种抗真菌能力，证实了防御机制依赖于活力。进一步分析表明，在大丽弧菌胁迫下，红细胞分泌一层增厚的富含果胶和细胞外DNA （exDNA）的粘液层，包裹真菌菌丝，形成物理屏障。棉花和玉米红细胞分泌物的代谢组学分析发现了一组保守的代谢物，包括与黄酮和黄酮醇生物合成、缬氨酸、亮氨酸和异亮氨酸代谢以及苯丙素生物合成有关的化合物，这些化合物可能有助于抵抗病原体的化学防御。这些发现揭示了红血球介导的抑制大丽花枯萎病的细胞和分子机制，并为制定棉花抗黄萎病育种策略提供了见解。

{"title":"The contribution of root border cells as a defense barrier against soil-borne pathogen Verticillium dahliae: Insights from the host cotton and the non-host corn","authors":"Sen Zhang , Xiaoyu Wang , Dan Zhang , Ruichi Hua, Yijin Yan, Juan Yang, Jinhu Ma, Jie Wang, Xiaohuan Yang","doi":"10.1016/j.micres.2026.128452","DOIUrl":"10.1016/j.micres.2026.128452","url":null,"abstract":"<div><div>Verticillium wilt can be caused by the soil-borne fungal pathogen <em>Verticillium dahliae</em> (<em>V. dahliae)</em>. It is a destructive vascular pathogen that infects more than 200 plant species, including economically important crops such as cotton. The disease induces severe symptoms such as wilting, chlorosis, and necrosis, ultimately resulting in substantial yield losses. Conventional management strategies, including chemical fungicides and crop rotation, have exhibited limited effectiveness against <em>V. dahliae</em>, emphasizing the urgent need to elucidate innate plant resistance mechanisms for breeding Verticillium-resistant varieties. In this study, the defense mechanisms of root border cells (RBCs) against <em>V. dahliae</em> were investigated. Fluorescence microscopy and cryo-scanning electron microscopy demonstrated that RBCs were viable and free cells, exhibiting round, intermediate, and elongated morphologies. <em>In vitro</em> co-culture assays revealed that viable RBCs isolated from cotton or corn markedly suppressed the growth of <em>V. dahliae</em>, whereas heat-inactivated RBCs lost this antifungal capacity, confirming that the defense mechanism was viability-dependent. Further analysis indicated that under <em>V. dahliae</em> stress, RBCs secreted a thickened mucilage layer enriched in pectin and extracellular DNA (exDNA), which encapsulated fungal hyphae and formed a physical barrier. Metabolomic profiling of RBC secretions from both cotton and corn identified a conserved set of metabolites, including compounds involved in flavone and flavonol biosynthesis, valine, leucine, and isoleucine metabolism, and phenylpropanoid biosynthesis, which could contribute to chemical defense against pathogens. These findings demonstrate the cellular and molecular mechanisms underlying RBC-mediated inhibition of <em>V. dahliae</em> infection and provide insights for developing Verticillium wilt resistance breeding strategies in cotton.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128452"},"PeriodicalIF":6.9,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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