The ISME Journal最新文献_第2页

Autoinducer-2-mediated communication network within human gut microbiota 人类肠道微生物群内的自诱导剂-2介导的通讯网络

The ISME Journal Pub Date : 2025-10-07 DOI: 10.1093/ismejo/wraf204

Qingying Fan, Hengxi Sun, Xueyuan Lin, Wenguang Yang, Xihui Shen, Lei Zhang

{"title":"Autoinducer-2-mediated communication network within human gut microbiota","authors":"Qingying Fan, Hengxi Sun, Xueyuan Lin, Wenguang Yang, Xihui Shen, Lei Zhang","doi":"10.1093/ismejo/wraf204","DOIUrl":"https://doi.org/10.1093/ismejo/wraf204","url":null,"abstract":"Quorum sensing (QS) is a chemical communication process that connects microbial members in various microbial systems. Bacterial communication networks mediated by QS play important roles in the regulation of intestinal microecological balance as well as nutrition and metabolism of the host. However, how human gut microbes utilize QS signals to communicate with one another remains largely unknown. In this study, we first examined the prevalence and abundance of genes encoding QS signal synthases in 3329 species representatives clustered from 289232 prokaryotic genomes in the Unified Human Gastrointestinal Genome collection. Our results show autoinducer-2 (AI-2) is the most prevalent QS signal within the human gut microbiota, with the synthase gene luxS being found in 2039 species mainly distributed within Firmicutes, Actinobacteriota, Bacteroidota, and Proteobacteria. Furthermore, 299 species carry genes encoding one or more types of AI-2 receptors (LuxP-, LsrB-, dCache_1-, and GAPES1-type). The dCache_1- and GAPES1-type receptors can function as methyl-accepting chemotaxis proteins, histidine kinases, c-di-GMP synthases and/or c-di-GMP-specific phosphodiesterases, serine phosphatases, and serine/threonine kinases, suggesting the diversity of AI-2-mediated interspecies communication modes among human gut microbiota. Metatranscriptomic analysis showed that a number of AI-2 synthase- and receptor-encoding genes can be expressed in the human gut in healthy and/or unhealthy states. The communication network analysis suggests that AI-2-mediated interactions widely occur among members of Firmicutes, Proteobacteria, Actinobacteriota, Campylobacterota, and Spirochaetota. Overall, this study deepens understanding of QS-mediated communication network among human gut microbiota, and provides guidance for engineering gut microbiota and constructing new synthetic microbial consortia based on complex microbial interactions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145241900","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

Half of microbial eukaryote literature focuses on only twelve human parasites. 一半的真核微生物文献只关注12种人类寄生虫。

The ISME Journal Pub Date : 2025-10-07 DOI: 10.1093/ismejo/wraf219

Joanna A Lepper,H B Beryl Rappaport,Angela M Oliverio

引用次数: 0

Temperature mediates biodiversity and metabolism of culturable lignocellulose-degrading consortia from intertidal wetlands. 温度调节潮间带湿地可培养木质纤维素降解菌群的生物多样性和代谢。

The ISME Journal Pub Date : 2025-10-04 DOI: 10.1093/ismejo/wraf218

Jiyu Chen,Min Yang,Qichao Tu,Lu Lin

{"title":"Temperature mediates biodiversity and metabolism of culturable lignocellulose-degrading consortia from intertidal wetlands.","authors":"Jiyu Chen,Min Yang,Qichao Tu,Lu Lin","doi":"10.1093/ismejo/wraf218","DOIUrl":"https://doi.org/10.1093/ismejo/wraf218","url":null,"abstract":"Coastal bacteria play an important role in the conversion of terrestrial organic carbon (TerrOC). However, their ecological patterns and drivers remains elusive. Here, 180 bacterial communities from 10 regions along the Chinese coastline, covering an 18,000 km transect between 18.27 °N and 39.82 °N, were cultured under three typical lignocellulosic substrates, hardwood (aspen), softwood (pine), and herbaceous (rice straw), respectively. All the consortia showed a broad spectrum of TerrOC utilization, and displayed degradation capacities comparable with those previously established though preliminary in situ lignocellulose enrichment. Moreover, following the metabolic theory of ecology, annual average temperature of the sites stimulated community metabolism, even though all were cultured at 30°C. Consortia enriched on aspen exhibited the highest temperature sensitivity. 16S rRNA gene amplicon and metatranscriptomic sequencing analyses revealed temperature-dependent latitudinal diversity gradients, displaying a trend that was opposite of the temperature-diversity positive relationship observed in terrestrial lignin-degrading microbes. The community composition shifted to adapt to rising environmental temperature. To enhance lignin degradation, aspen consortia from high annual average temperature employed metabolic generalists, which induced expression of dypB centered gene families for lignin depolymerization and versatile pathways for degradation of lignin derivates. This study reveals the intrinsic drivers for coastal cultured lignocellulose degrading bacterial communities from an ecological perspective and deepens our understanding of the metabolic mechanisms in coastal TerrOC conversion.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"97 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215840","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

Microbial interactions between climate warming and antimicrobial resistance threaten soil carbon storage and global health 气候变暖和抗菌素耐药性之间的微生物相互作用威胁着土壤碳储存和全球健康

The ISME Journal Pub Date : 2025-10-04 DOI: 10.1093/ismejo/wraf220

Shamik Roy, Marc G Dumont, James A Bradley, Marcela Hernández

引用次数: 0

Deciphering the Universal Role of Gut Microbiota in Pollutant Transformation. 解读肠道微生物群在污染物转化中的普遍作用。

The ISME Journal Pub Date : 2025-09-30 DOI: 10.1093/ismejo/wraf215

Rui Hou,Xiaowei Jin,Jingchun Feng,Jingchuan Xue,Chengzhi Chen,Yuanqiang Zou,Xiangrong Xu,Kefu Yu,Pei-Yuan Qian,Wei Zhang,Jizhong Zhou,Si Zhang,Zhifeng Yang

{"title":"Deciphering the Universal Role of Gut Microbiota in Pollutant Transformation.","authors":"Rui Hou,Xiaowei Jin,Jingchun Feng,Jingchuan Xue,Chengzhi Chen,Yuanqiang Zou,Xiangrong Xu,Kefu Yu,Pei-Yuan Qian,Wei Zhang,Jizhong Zhou,Si Zhang,Zhifeng Yang","doi":"10.1093/ismejo/wraf215","DOIUrl":"https://doi.org/10.1093/ismejo/wraf215","url":null,"abstract":"The gut microbiota represents a critical yet underexplored \"second genome\" in the host that functions as a key driver of pollutant transformation across Earth's ecosystems. This review synthesizes current understanding of over 490 pollutants across a wide range of species, highlighting the universal role of gut microbial communities in modifying pollutant exposure. We demonstrated that gut microbial communities transform a broad spectrum of environmental pollutants through evolutionarily conserved pathways, fundamentally altering their bioavailability, fate and toxicity potential within the host. Transformation reactions are elucidated with connections among the metabolic enzymes that are developed by specific gut microbes, emphasizing the markedly specific and complementary signatures of microbial biotransformation compared with the host process. By integrating multidisciplinary studies, the complex and dynamic interplay between the gut microbiota, host physiology, and environmental pollutants have been elucidated, and the drivers involved in the biotransformation processes have been proposed. Furthermore, current methodologies are critically evaluated and next-generation approaches to reveal the underlying mechanisms of gut microbiota-driven pollutant transformation are outlined. This review underscores the urgent need to systematize research on \"pollutant-gut microbiota-host\" interactions and advocates the integration of gut microbial perspectives into interdisciplinary research paradigms of toxicology, microbiology, and ecology.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145188961","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

Seasonal variability in community structure and metabolism of active deep-sea microorganisms. 深海活性微生物群落结构和代谢的季节变化。

The ISME Journal Pub Date : 2025-09-23 DOI: 10.1093/ismejo/wraf214

Yinghui He,Federico Baltar,Yong Wang

{"title":"Seasonal variability in community structure and metabolism of active deep-sea microorganisms.","authors":"Yinghui He,Federico Baltar,Yong Wang","doi":"10.1093/ismejo/wraf214","DOIUrl":"https://doi.org/10.1093/ismejo/wraf214","url":null,"abstract":"Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate with nutrient source variations as reflected by the different levels of microbial network complexity between two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117072","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

Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics. 嗜麦芽窄养单胞菌通过降解其脂肽类抗生素阻碍芽孢杆菌对番茄枯萎病的生物防治。

The ISME Journal Pub Date : 2025-09-23 DOI: 10.1093/ismejo/wraf210

Junwei Peng,Dmitri V Mavrodi,Jiasui Li,Suhelen Egan,Huanhuan Zhang,Xiuli Fan,Yang Liu,Keke Dang,Olga V Mavrodi,Qin Liu,Yuanhua Dong,Jiangang Li

{"title":"Stenotrophomonas maltophilia impedes Bacillus biocontrol of tomato wilt disease by degrading its lipopeptide antibiotics.","authors":"Junwei Peng,Dmitri V Mavrodi,Jiasui Li,Suhelen Egan,Huanhuan Zhang,Xiuli Fan,Yang Liu,Keke Dang,Olga V Mavrodi,Qin Liu,Yuanhua Dong,Jiangang Li","doi":"10.1093/ismejo/wraf210","DOIUrl":"https://doi.org/10.1093/ismejo/wraf210","url":null,"abstract":"Harnessing antibiotic-producing microorganisms that antagonize pathogens represents a sustainable approach for plant disease management. However, biocontrol agents that are effective in the laboratory often have diminished or variable performance in the field. It is often assumed that microbial interactions within the plant rhizosphere can influence the performance of biocontrol agents. To validate this hypothesis, we established a tripartite bacterial model system based on field investigations, involving antibiotic producers (Bacillus amyloliquefaciens P224, Bacillus subtilis P165, and Bacillus velezensis P63), an antibiotic degrader (Stenotrophomonas maltophilia P373), and a bacterial plant pathogen (Ralstonia solanacearum PA1). The selected Bacillus species antagonize R. solanacearum and act as biocontrol agents of the bacterial wilt of tomatoes caused by this pathogen. We demonstrated that S. maltophilia diminished this biocontrol effect by degrading the lipopeptide antibiotics iturin, fengycin, and surfactin secreted by Bacillus spp., thereby serving as a \"pathogen helper\" that indirectly facilitated pathogen invasion. Further transcriptomic and proteomic analyses revealed that the lipopeptide inactivation mechanism in S. maltophilia involved multi-drug efflux systems, ribosomal adaptation, and enzymatic hydrolysis. Additionally, the interspecies interactions in our model system are modulated by nutrient availability, with elevated carbon sources enhancing the interference competitive ability of Bacillus spp. against S. maltophilia, thereby mitigating its negative impact on the biocontrol of R. solanacearum. Our study sheds light on the complex interactions among plant pathogens, biocontrol agents, and the indigenous microbial community, underscoring the necessity to account for native antibiotic-degrading organisms when applying biocontrol strategies for effective disease management.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145117073","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

Synergistic interaction between microbial nitrogen fixation and iron reduction in the environment. 环境中微生物固氮与铁还原的协同作用。

The ISME Journal Pub Date : 2025-09-22 DOI: 10.1093/ismejo/wraf212

Xiaohan Liu,Ping Li,Keman Bao,Yaqi Wang,Helin Wang,Yanhong Wang,Zhou Jiang,Yi Yang,Songhu Yuan,Andreas Kappler,Yanxin Wang

{"title":"Synergistic interaction between microbial nitrogen fixation and iron reduction in the environment.","authors":"Xiaohan Liu,Ping Li,Keman Bao,Yaqi Wang,Helin Wang,Yanhong Wang,Zhou Jiang,Yi Yang,Songhu Yuan,Andreas Kappler,Yanxin Wang","doi":"10.1093/ismejo/wraf212","DOIUrl":"https://doi.org/10.1093/ismejo/wraf212","url":null,"abstract":"Nitrogen and iron are essential yet often limiting nutrients in many ecosystems. Microbial nitrogen fixation by diazotrophs and dissimilatory ferric iron reduction are key processes that sustain nitrogen and iron availability. However, their interactions are not well understood. Here, we demonstrate a synergistic relationship between microbial nitrogen fixation and ferric iron reduction, observed in both laboratory cultures and environmental samples. In diazotrophic ferric iron-reducing bacteria, including Klebsiella grimontii N7 and Geobacter sulfurreducens PCA, nitrogen fixation enhanced heterotrophic ferric iron-reducing rates by 14.7- and 2.69-fold, respectively, and ferric iron reduction concurrently increased 15N2 fixation by up to 100%. A similar synergy was observed in an interspecies system comprising the diazotroph Azospirillum humicireducens SgZ-5 T and the dissimilatory ferric iron-reducing bacterium Shewanella oneidensis MR-1. Transcriptomic analysis revealed that nitrogen fixation upregulated pathways involved in carbon and nitrogen metabolism, including amino acid biosynthesis, glycolysis, and the tricarboxylic acid cycle (P < 0.01), thereby accelerating ferric iron reduction through nitrogen supply. In turn, ferric iron reduction stimulated organic carbon oxidation, generating the energy and reducing equivalents needed for microbial nitrogen fixation. These findings were further validated through microcosm experiments and meta-omics analyses of environmental samples from aquifers, marine sediments, hot springs, and soils, providing new insights into the coupled nitrogen, iron, and carbon cycles in natural ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103567","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

Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants. 下水道微生物群塑造了污水处理厂的微生物群落组成和动态。

The ISME Journal Pub Date : 2025-09-22 DOI: 10.1093/ismejo/wraf213

Marie Riisgaard-Jensen,Rodrigo Maia Valença,Miriam Peces,Per Halkjær Nielsen

{"title":"Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.","authors":"Marie Riisgaard-Jensen,Rodrigo Maia Valença,Miriam Peces,Per Halkjær Nielsen","doi":"10.1093/ismejo/wraf213","DOIUrl":"https://doi.org/10.1093/ismejo/wraf213","url":null,"abstract":"The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that it harbors a process-critical activated sludge microbes, thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed the hypothesis that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut-bacteria in the wastewater upstream to prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plants inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as the sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source community for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103568","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

Humin oxidation drives microbial dehalogenation in oligotrophic environments 贫营养环境中腐殖质氧化驱动微生物脱卤

The ISME Journal Pub Date : 2025-09-19 DOI: 10.1093/ismejo/wraf207

Zimeng Zhang, Xing Liu, Zhiling Li, Xueqi Chen, Yunxia Zu, Shih-Hsin Ho, Bin Liang, Shungui Zhou, Aijie Wang

{"title":"Humin oxidation drives microbial dehalogenation in oligotrophic environments","authors":"Zimeng Zhang, Xing Liu, Zhiling Li, Xueqi Chen, Yunxia Zu, Shih-Hsin Ho, Bin Liang, Shungui Zhou, Aijie Wang","doi":"10.1093/ismejo/wraf207","DOIUrl":"https://doi.org/10.1093/ismejo/wraf207","url":null,"abstract":"Energy acquisition presents a fundamental constraint for microbial survival in oligotrophic environments. Although heterotrophic organohalide-respiring bacteria (OHRB) are known to perform reductive dehalogenation in organohalide-contaminated oligotrophic ecosystems, their energy metabolism remains poorly understood. Here, we report that Pseudomonas sp. CP-1, an OHRB, can directly oxidize humin from diverse oligotrophic aquifers to drive organohalide respiration. Spectroscopy, electrochemistry and metabolic profiling demonstrated that electrons stored in phenolic hydroxyl and amino groups of humin were utilized by strain CP-1 for organohalide respiration. Mutational and chemical inhibition studies identified an extracellular electron uptake pathway involving a multiheme cytochrome EeuP, which transfers extracellular electrons into the organohalide-respiratory chain, thereby coupling humin oxidation with reductive dehalogenation. Phylogenetic analyses revealed the widespread distribution of EeuP homologs across environmental bacterial taxa, implying a broader ecological relevance. This discovery sheds light on the hidden world of subsurface microbiology, with implications for understanding microbial energy metabolism in the energy-scarce environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089629","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