The ISME Journal最新文献_第5页

Multi-Scale Evidence for Declining Microbial Carbon Fixation Along Forest Succession Gradients 森林演替梯度微生物固碳下降的多尺度证据

The ISME Journal Pub Date : 2025-08-24 DOI: 10.1093/ismejo/wraf191

Shu-Yi-Dan Zhou, Zhiyang Lie, Chaotang Lei, Qi Zhang, Xujun Liu, Guopeng Wu, Roy Neilson, Fu-Yi Huang, Guowei Chu, Ze Meng, Dong Zhu, David T Tissue, Josep Peñuelas, Juxiu Liu

{"title":"Multi-Scale Evidence for Declining Microbial Carbon Fixation Along Forest Succession Gradients","authors":"Shu-Yi-Dan Zhou, Zhiyang Lie, Chaotang Lei, Qi Zhang, Xujun Liu, Guopeng Wu, Roy Neilson, Fu-Yi Huang, Guowei Chu, Ze Meng, Dong Zhu, David T Tissue, Josep Peñuelas, Juxiu Liu","doi":"10.1093/ismejo/wraf191","DOIUrl":"https://doi.org/10.1093/ismejo/wraf191","url":null,"abstract":"Although soil carbon accumulates during subtropical forest succession, changes in microbial communities and their carbon fixation capacity remain unclear. Using an integrative approach that combines field experimentation, extensive global metagenomic data, and isotope labelling, we analyzed 84 soil microbiomes from a long-term successional site and 755 global metagenomes to investigate microbial community dynamics and their role in carbon fixation. Based on field data, bacteria, fungi, and protists had synchronous succession with vegetation; however, the relative abundance of carbon fixation genes declined significantly in later successional stages. To further investigate this outcome, we analyzed global data from planted and mature natural forests and found significantly higher carbon fixation potential in planted forests, predominantly driven by Pseudomonadota and Actinomycota members. Field-based 13C labelling results further confirmed a significant decline in microbial CO₂ fixation rates with forest succession. These findings underscore the ecological importance of microbial carbon fixation in early forest succession, emphasizing its foundational role in initiating soil carbon accumulation and shaping long-term carbon cycling trajectories.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900124","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

Protists as determinants of the One Health framework 原生生物是一个健康框架的决定因素

The ISME Journal Pub Date : 2025-08-22 DOI: 10.1093/ismejo/wraf179

Alejandro Berlinches de Gea, Julia Walochnik, Jens Boenigk, Kenneth Dumack, Fiona Henriquez-Mui, Sonja Rückert, Martin Simon, Stefan Geisen

引用次数: 0

Timescale of environmental change modulates metabolic guild cohesion in microbial communities 环境变化的时间尺度调节微生物群落代谢导向内聚

The ISME Journal Pub Date : 2025-08-22 DOI: 10.1093/ismejo/wraf186

Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn

{"title":"Timescale of environmental change modulates metabolic guild cohesion in microbial communities","authors":"Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn","doi":"10.1093/ismejo/wraf186","DOIUrl":"https://doi.org/10.1093/ismejo/wraf186","url":null,"abstract":"Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding how microbial populations respond to these changes is critical for predicting the impact of perturbations, interventions, and climate change on communities. Because communities typically harbor tens to hundreds of distinct taxa, the response of microbial abundances to perturbations is potentially complex. However, even though taxonomic diversity is high, in many communities taxa can be grouped into metabolic guilds of strains with similar metabolic traits. These guilds effectively reduce the complexity of the system by providing a physiologically motivated coarse-graining. Here, using a combination of simulations, theory, and experiments, we show that the response of guilds to nutrient fluctuations depends on the timescale of those fluctuations. Rapid changes in nutrient levels drive cohesive, positively correlated abundance dynamics within guilds. For slower timescales of environmental variation, members within a guild begin to compete due to similar resource preferences, driving negative correlations in abundances between members of the same guild. Our results provide a route to understanding the relationship between metabolic guilds and community response to changing environments, as well as an experimental approach to discovering metabolic guilds via designed nutrient perturbations to communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900359","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

Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities 基于个体的建模（IbM）揭示了细菌群落中的空间和社会相互作用

The ISME Journal Pub Date : 2025-08-21 DOI: 10.1093/ismejo/wraf116

Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F M Van Impe

{"title":"Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities","authors":"Jian Wang, Ihab Hashem, Satyajeet Bhonsale, Jan F M Van Impe","doi":"10.1093/ismejo/wraf116","DOIUrl":"https://doi.org/10.1093/ismejo/wraf116","url":null,"abstract":"Bacterial interactions are fundamental in shaping community structure and function, driving processes that range from plastic degradation in marine ecosystems to dynamics within the human gut microbiome. Yet, studying these interactions is challenging due to difficulties in resolving spatiotemporal scales, quantifying interaction strengths, and integrating intrinsic cellular behaviors with extrinsic environmental conditions. Individual-based modeling addresses these challenges through single-cell-level simulations that explicitly model growth, division, motility, and environmental responses. By capturing both the spatial organization and social interactions, individual-based modeling reveals how microbial interactions and environmental gradients collectively shape community architecture, species coexistence, and adaptive responses. In particular, individual-based modeling provides mechanistic insights into how social behaviors—such as competition, metabolic cooperation, and quorum sensing—are regulated by spatial structure, uncovering the interplay between localized interactions and emergent community properties. In this review, we synthesize recent applications of individual-based modeling in studying bacterial spatial and social interactions, highlighting how their interplay governs community stability, diversity, and resilience. By linking individual-scale interactions with the ecosystem-level organization, individual-based modeling offers a predictive framework for understanding microbial ecology and informing strategies for controlling and engineering bacterial consortia in both natural and applied settings.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A case for absolute gene expression estimates in microbiome studies using metatranscriptomics 在微生物组研究中使用亚转录组学估计绝对基因表达的案例

The ISME Journal Pub Date : 2025-08-21 DOI: 10.1093/ismejo/wraf188

Michiel Perneel, Harriet Alexander, Pascal I Hablützel, Steven Maere

引用次数: 0

Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils 生物炭抑制肥料改良土壤中抗生素抗性基因的共轭转移

The ISME Journal Pub Date : 2025-08-21 DOI: 10.1093/ismejo/wraf187

Jing Fang, Zhiwen Chen, Zhigang Yu, Shengdao Shan, Yucheng Hou, Lili Liu, Jin Huang, Bing Li, Jianhua Guo

{"title":"Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils","authors":"Jing Fang, Zhiwen Chen, Zhigang Yu, Shengdao Shan, Yucheng Hou, Lili Liu, Jin Huang, Bing Li, Jianhua Guo","doi":"10.1093/ismejo/wraf187","DOIUrl":"https://doi.org/10.1093/ismejo/wraf187","url":null,"abstract":"The environmental dissemination of antibiotic resistance genes (ARGs), particularly in manure-amended soils, poses a growing threat to public health due to the potential transfer of ARGs to humans and animals. Effective strategies are urgently needed to mitigate ARG spread in agricultural settings. Biochar, an eco-friendly soil amendment, shows promise for pollution control, yet its role in suppressing ARG horizontal gene transfer remains unclear. Here, metagenomic analysis showed that manure application significantly increased the relative abundance of ARGs in soil microbiota, whereas biochar amendment reduced it. To determine whether biochar suppresses ARG dissemination by inhibiting horizontal transfer, we established a soil microcosm. Manure application increased the conjugative transfer ratio by 3-fold, whereas biochar effectively suppressed this transfer reducing it to levels observed in unamended soils. Cell sorting and 16S rRNA gene amplicon sequencing demonstrated that biochar treatment reduced the diversity of transconjugant pools at both phylum and genus level. Transconjugants were primarily affiliated with Pseudomonadota, Bacillota, and Actinomycetota, with Massilia, Delftia, and Ammoniphilus being the most abundant genera in biochar treatment soil. Mechanistic investigations revealed that biochar-mediated inhibition of ARG transfer was linked to reduced ATP energy supply, decreased reactive oxygen species production, and lower cell membrane permeability, and diminished bioavailability of heavy metals and antibiotics. Additionally, biochar altered soil enzyme activity and microbial community structure, further limiting ARG dissemination. The findings provide insights into biochar-induced mitigation of ARG spread in manure-amended soils and highlight its potential as an effective strategy for controlling environmental ARG transmission.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900133","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

Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont 在运动、木质纤维素消化和氮代谢方面的功能分工揭示了双歧菌的存在

The ISME Journal Pub Date : 2025-08-20 DOI: 10.1093/ismejo/wraf178

Jieyang Fu, Yiting Liu, Takuya Yoshioka, Katsura Igai, Takako Mabuchi, Kumiko Kihara, Takumi Murakami, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh

{"title":"Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont","authors":"Jieyang Fu, Yiting Liu, Takuya Yoshioka, Katsura Igai, Takako Mabuchi, Kumiko Kihara, Takumi Murakami, Nathan Lo, Moriya Ohkuma, Yuichi Hongoh","doi":"10.1093/ismejo/wraf178","DOIUrl":"https://doi.org/10.1093/ismejo/wraf178","url":null,"abstract":"Mixotricha paradoxa is a large, cellulolytic flagellate present in the hindgut of the termite Mastotermes darwiniensis. This parabasalid flagellate is unique in its reliance on ectosymbiotic spirochetes for motility. We analyzed the transcriptome of M. paradoxa and the genomes of the ectosymbiotic spirochete Propulsinema mixotrichae (“Treponematales”), the rod-shaped ectosymbiont Synergitannerella mixotrichae (Bacteroidales), and the endosymbiont Endomicrobiellum mixotrichae (Endomicrobiales), all of which are obligately associated with M. paradoxa and were taxonomically described in this study. Mixotricha paradoxa highly expressed genes for diverse glycoside hydrolases (GHs) and likely ferments sugars to H2, CO2, acetate, ethanol, and glycerol. Similar to the case for parasitic parabasalids such as Trichomonas vaginalis, transcripts for biosynthesis of nucleotides and many amino acids were not detected in our analyses of M. paradoxa. Propulsinema mixotrichae possesses genes encoding proteins for the assembly of flagella and for those in pathways associated with chemotaxis and dinitrogen fixation. Such genes are absent in Syn. mixotrichae, which instead possesses numerous genes encoding GH enzymes, which are largely complementary to the GH repertoire of M. paradoxa. Endomicrobiellum mixotrichae appears to provide nucleotides and nine amino acids to its host, which in turn likely supplies three amino acids, including tryptophan, to Endo. mixotrichae. Because bacterial cells, in addition to wood particles, were observed in food vacuoles of M. paradoxa, these ecto- and endosymbionts may be digested by the flagellate host. Overall, the distinct roles of each symbiont highlight the efficient functional division of labor that has evolved in this holobiont.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900367","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

Vitamin auxotrophies shape microbial community assembly on model marine particles 维生素营养不良形成微生物群落组装在模型海洋颗粒

The ISME Journal Pub Date : 2025-08-20 DOI: 10.1093/ismejo/wraf184

Rachel Gregor, Gabriel T Vercelli, Rachel E Szabo, Matti Gralka, Ryan C Reynolds, Evan B Qu, Naomi M Levine, Otto X Cordero

{"title":"Vitamin auxotrophies shape microbial community assembly on model marine particles","authors":"Rachel Gregor, Gabriel T Vercelli, Rachel E Szabo, Matti Gralka, Ryan C Reynolds, Evan B Qu, Naomi M Levine, Otto X Cordero","doi":"10.1093/ismejo/wraf184","DOIUrl":"https://doi.org/10.1093/ismejo/wraf184","url":null,"abstract":"Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism represents only a small fraction of the biosynthetic repertoire of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored in their potential to shape microbial communities. Here, we focus on B vitamin exchange in marine bacterial communities that degrade polysaccharides, a key component of particulate organic matter. We found that in a screen of 150 natural isolates, almost a third were auxotrophs for one or more B vitamins. By measuring physiological parameters like uptake affinities and comparing those to ambient seawater concentrations, we showed that marine bacteria live at the edge of vitamin limitation in the environment. To understand how auxotrophs survive in the open oceans, we used our experimental data to model vitamin cross-feeding on particles through both secretion and lysis. Our results highlight the importance of vitamin auxotrophies in shaping microbial community assembly and succession, adding another layer of complexity to the trophic structure of particle-associated communities.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900364","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

Liberation of galactose from lactose by gut microbial β-galactosidase prevents uterine bacterial infection 肠道微生物β-半乳糖苷酶从乳糖中释放半乳糖，防止子宫细菌感染

The ISME Journal Pub Date : 2025-08-20 DOI: 10.1093/ismejo/wraf185

Jiapei Cai, Yuhang He, Linkai Qu, Jiuxi Liu, Xufeng Xie, Yongguo Cao

{"title":"Liberation of galactose from lactose by gut microbial β-galactosidase prevents uterine bacterial infection","authors":"Jiapei Cai, Yuhang He, Linkai Qu, Jiuxi Liu, Xufeng Xie, Yongguo Cao","doi":"10.1093/ismejo/wraf185","DOIUrl":"https://doi.org/10.1093/ismejo/wraf185","url":null,"abstract":"Reproductive infection is closely associated with adverse reproductive outcomes, contributing to a reduced live birth rate per pregnancy and an elevated infertility rate. Nutrition is widely acknowledged as a fundamental determinant of human and animal health, as well as the etiopathogenesis of various diseases, with the gut microbiota playing an integral part in this process. Lactose, a disaccharide present in mammalian milk, has been identified as a potential prebiotic. Here, we found that lactose was able to mitigate the inflammatory response elicited by uterine bacterial infection, preserve the integrity of the endometrial epithelial barrier, and reduce the bacterial load in the uterus. The protective effects of lactose were found to be gut microbiota-dependent and fecal microbiota transplantation from lactose-treated mice to recipient mice also ameliorated E. coli-induced metritis. 16S rRNA gene amplicon sequencing revealed that lactose supplementation changed the gut microbiota, specifically increasing the abundance of Lactobacillus intestinalis (L. intestinalis). Whole-genome sequencing identified that L. intestinalis expressed β-galactosidase, a lactose-metabolizing enzyme. Inhibition or exogenous supplementation of β-galactosidase confirmed its essential role in mediating lactose’s protective effects against E. coli uterine infection. Furthermore, intragastric administration of [1-13Cgal]-lactose confirmed that galactose, a lactose metabolite, could translocate from the gut to the uterus. Mechanistically, galactose upregulated the CEBPB-dependent S100a8 expression after E. coli infection, and the protective effect could be blunted by S100a8 inhibition. Collectively, these findings highlight a nutrition-microbiota-host interaction that is stimulated by lactose supplementation, providing potential benefits for reproductive infection.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900365","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

Dysbiotic gut fungi exacerbate Klebsiella peumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation. 益生菌通过dectin -1介导的肺泡巨噬细胞过度活化加剧肺炎克雷伯菌肺部感染。

The ISME Journal Pub Date : 2025-08-16 DOI: 10.1093/ismejo/wraf181

Shengfu He,Yating Sun,Jiawen Yu,Mingyang Tang,Qingyue Zhang,Bao Meng,Renyu Fan,Zhiqiang Liu,Yanyan Liu,Lifen Hu,Ting Wu,Jiabin Li

{"title":"Dysbiotic gut fungi exacerbate Klebsiella peumoniae lung infection via Dectin-1-mediated alveolar macrophage hyperactivation.","authors":"Shengfu He,Yating Sun,Jiawen Yu,Mingyang Tang,Qingyue Zhang,Bao Meng,Renyu Fan,Zhiqiang Liu,Yanyan Liu,Lifen Hu,Ting Wu,Jiabin Li","doi":"10.1093/ismejo/wraf181","DOIUrl":"https://doi.org/10.1093/ismejo/wraf181","url":null,"abstract":"Escalating antibiotic resistance of Klebsiella pneumoniae underscores the urgent need for therapeutic strategies. Whereas gut bacterial dysbiosis exacerbates pulmonary infections, the role of gut fungi in modulating lung immunity remains understudied. Here, we demonstrate that antibiotic-induced gut fungal expansion aggravates pneumonia by enhancing alveolar macrophage-driven inflammation via Dectin-1 signaling. Clinical analyses demonstrated that pneumonia patients receiving ineffective prehospital antibiotic therapy showed gut bacterial depletion accompanied by fungal overgrowth (primarily Candida spp.), with a positive correlation observed between fungal abundance and hospitalization duration. In murine models, antibiotic-induced gut microbiota disruption promoted fungal proliferation, subsequently upregulating Dectin-1 expression in alveolar macrophages. This activation triggered excessive IL-1β secretion and neutrophil recruitment, exacerbating lung injury and mortality. Our results demonstrated that both antifungal intervention and Dectin-1 knockout reversed these pathological effects, resulting in improved survival rates, reduced bacterial dissemination, and attenuated inflammatory cytokine levels. Mechanistically, gut fungi remotely potentiated pulmonary inflammation through the alveolar macrophage \"Dectin-1/IL-1β/neutrophil axis\", independent of pathogen clearance. Although recent studies have begun to uncover \"mycobiome-lung\" disease associations, our findings specifically demonstrate that fungal dysbiosis mediates the \"gut-lung axis\" during multidrug-resistant Klebsiella pneumoniae infections. This study provides mechanistic insights into microbial crosstalk and advances translational approaches for combating antibiotic-exacerbated pneumonias.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144857670","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