The ISME Journal最新文献

{"title":"High life history diversity within a single genus of algal viruses","authors":"Eva J P Lievens, Irina V Agarkova, David D Dunigan, James L Van Etten, Lutz Becks","doi":"10.1093/ismejo/wraf146","DOIUrl":"https://doi.org/10.1093/ismejo/wraf146","url":null,"abstract":"Microbial viruses are key players in aquatic ecosystems, where they control host populations and affect nutrient flow. The impact of these viruses can be understood through their life history traits, which are used to parameterize ecological models and infer evolutionary strategies. However, most existing data on microbial virus traits come from highly divergent strains. Very little is known about the trait diversity of closely related viruses, opening the critical question: can unknown viral traits be extrapolated from those of known strains? To answer this question, we quantified the life history diversity of related aquatic microbial viruses in unprecedented detail. We measured nine life history traits in 34 strains belonging to the phytoplankton-infecting genus Chlorovirus. Chloroviral traits varied 5- to 77-fold across strains, in some cases rivaling the known trait range for all phytoplankton viruses. Contrary to expectations, only specific infectivity was predictive of viral growth and there was no evidence of life history trade-offs. Our results suggest that more detailed studies of viral diversity could change our understanding of their function in aquatic ecosystems. More broadly, we show that known virus strains may not be representative of their relatives.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577950","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}

{"title":"GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities","authors":"J Pamela Engelberts, Jun Ye, Donovan H Parks, Eilish S McMaster, Allison S McInnes, Ben J Woodcroft, James G Volmer, Simon J McIlroy, Gene W Tyson","doi":"10.1093/ismejo/wraf138","DOIUrl":"https://doi.org/10.1093/ismejo/wraf138","url":null,"abstract":"Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualising certain lineages, and the​​ design and optimis​ation of​ new probes is time consuming and does not scale​ to the ​known​ diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are ​obtained ​from environmental or clinical samples through fluorescence activated single-cell sorting (FACS). GenomeFISH can ​distinguish between ​strains with up to 99% average nucleotide identity and was successfully applied to visualise strains in mock communities and human faecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualisation of complex microbial systems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568600","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}

{"title":"Targeting Catenibacterium mitsuokai with icariin modulates gut microbiota and improves hepatic lipid metabolism in intrauterine growth restriction.","authors":"Yusen Wei,Jiangdi Mao,Wenjie Tang,Yanfei Ma,Jiachen Li,Songtao Su,Zhixiang Ni,Jinhong Wu,Daren Liu,Haifeng Wang","doi":"10.1093/ismejo/wraf141","DOIUrl":"https://doi.org/10.1093/ismejo/wraf141","url":null,"abstract":"Male offspring with intrauterine growth restriction exhibit more pronounced hepatic lipid metabolism abnormalities than females, necessitating earlier intervention. Icariin has been shown to effectively modulate hepatic lipid metabolism in male piglets with intrauterine growth restriction. However, the role of gut microbiota in this process remains to be elucidated. This study aimed to explore the influence of gut microbiota on icariin-induced enhancement of hepatic lipid metabolism. By examining changes in microbiota composition and hepatic lipid metabolism following icariin intervention, the study demonstrated an association between microbial alterations and hepatic lipid regulation through fecal microbiota transplantation. The impact of Catenibacterium on gut microbiota structure and hepatic lipid metabolism was assessed in vivo, and the direct effect of icariin on Catenibacterium was explored in vitro. Results revealed that icariin intervention modified fecal, ileal, and colonic microbiota in male piglets with intrauterine growth restriction, enhanced gut morphology and barrier function, and normalized the expression of hepatic peroxisome proliferator-activated receptor (PPAR) signaling pathway-related genes. Fecal microbiota transplantation from piglets with intrauterine growth restriction impaired intestinal barrier function and led to hepatic lipid deposition, whereas transplantation from icariin-treated donors showed no pathological changes, an outcome associated with reduced abundance of Catenibacterium. Mechanistically, icariin inhibits adenosine triphosphate synthesis to suppress Catenibacterium, remodels gut microbiota, reduces lipopolysaccharide production and translocation, and activates the hepatic PPARα/CD36 axis. In conclusion, icariin intervention alleviates hepatic lipid metabolic disorders in male offspring with intrauterine growth restriction by suppressing Catenibacterium, restoring gut microbial balance, and enhancing intestinal barrier integrity to limit lipopolysaccharide translocation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547705","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}

{"title":"Functional team selection as a framework for local adaptation in plants and their belowground microbiomes.","authors":"Nancy Collins Johnson,César Marín","doi":"10.1093/ismejo/wraf137","DOIUrl":"https://doi.org/10.1093/ismejo/wraf137","url":null,"abstract":"Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some -but not all - circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: 1) selective force, 2) host constitution, 3) microbial diversity, and 4) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533616","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}

{"title":"Fungal hyphae promote bacterial contact-dependent killing during surface-associated growth.","authors":"Miao Han,Chujin Ruan,Gang Wang,David R Johnson","doi":"10.1093/ismejo/wraf135","DOIUrl":"https://doi.org/10.1093/ismejo/wraf135","url":null,"abstract":"Bacterial contact-dependent killing in spatially structured systems is shaped by physical constraints and biological interactions. In this study, we demonstrate the importance of fungal hyphae in facilitating bacterial dispersal and promoting contact-dependent killing during surface-associated growth. Using Vibrio cholerae as a killing bacterium and Pseudomonas stutzeri as a target bacterium, we show that fungal hyphae act as dispersal agents that facilitate bacterial spatial intermixing and promote contact-dependent killing. Specifically, we show that dispersal along fungal hyphae increases the number of contacts between V. cholerae and P. stutzeri cells, which in turn increases the extent of killing via the type VI secretion system (T6SS) encoded by V. cholerae. This enables V. cholerae to achieve growth dominance despite initial population disadvantages. We further show that the effect of fungal hyphae on the killing efficacy of V. cholerae depends on flagellar motility. Our study underscores the multifaceted effects of fungal hyphae in enhancing bacterial dispersal and intensifying interspecies interactions, highlighting the ecological significance of fungal-bacterial interactions in spatially structured systems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533617","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}

{"title":"Diverse rhizospheric Bacillus are required for protection against a leaf pathogen","authors":"Amal Ghosheh, Moshe Alon, Shay Kenneth-Mordoch, Ziv Kleinman, Marnix H Medema, Omri M Finkel","doi":"10.1093/ismejo/wraf134","DOIUrl":"https://doi.org/10.1093/ismejo/wraf134","url":null,"abstract":"The microbiota plays a crucial role in protecting plants from pests and pathogens, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant–soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae pv. tomato DC3000. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. Applying inocula with high within-genus diversity offers a significant improvement to current biocontrol strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144533136","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}

{"title":"Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching","authors":"Angie Mordant, J Alfredo Blakeley-Ruiz, Manuel Kleiner","doi":"10.1093/ismejo/wraf127","DOIUrl":"https://doi.org/10.1093/ismejo/wraf127","url":null,"abstract":"Diet has strong impacts on the composition and function of the gut microbiota with implications for host health. Therefore, it is critical to identify the dietary components that support growth of specific microorganisms in vivo. We used protein-based stable isotope fingerprinting (Protein-SIF) to link microbial species in gut microbiota to their carbon sources by measuring each microorganism’s natural 13C content (δ13C) and matching it to the 13C content of available substrates. We fed gnotobiotic mice, inoculated with a 13 member microbiota, diets in which the 13C content of all components was known. We varied the source of protein, fiber or fat to observe 13C signature changes in microbial consumers of these substrates. We observed significant changes in the δ13C values and abundances of specific microbiota species, as well as host proteins, in response to changes in 13C signature or type of protein, fiber, and fat sources. Using this approach we were able to show that upon switching dietary source of protein, fiber, or fat (1) some microbial species continued to obtain their carbon from the same dietary component (e.g., protein); (2) some species switched their main substrate type (e.g., from protein to carbohydrates); and (3) some species might derive their carbon through foraging on host compounds. Our results demonstrate that Protein-SIF can be used to identify the dietary-derived substrates assimilated into proteins by microorganisms in the intestinal tract; this approach holds promise for the analysis of microbiome substrate usage in humans without the need of substrate labeling.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144513138","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}

{"title":"Endofungal Bacteria as Hidden Facilitators of Biotic Interactions","authors":"Ingrid Richter, Hannah Büttner, Christian Hertweck","doi":"10.1093/ismejo/wraf128","DOIUrl":"https://doi.org/10.1093/ismejo/wraf128","url":null,"abstract":"Fungi play pivotal roles in ecology and human health, driving nutrient cycling, supporting antibiotic production, and posing threats through toxin production. Less well-recognized, however, is their ability to harbour endosymbiotic bacteria. Advances in genomics and microscopy have revealed the prevalence of endofungal bacteria across diverse fungal phyla, though their functions are primarily inferred from genomic and transcriptomic studies. Recent functional research has begun to shed light on their influence on fungal pathogenicity, physiology, and ecology. These findings raise fundamental questions about the establishment and benefits of bacterial-fungal endosymbiosis, as well as the role of endosymbionts in mediating fungal interactions with other organisms. This review provides an in-depth analysis of the molecular mechanisms involved in the establishment and persistence of these symbioses. It also summarizes the current understanding of how endofungal bacteria impact fungal interactions with other organisms. For instance, endofungal bacteria contribute to the beneficial effects of fungi on plant health and fitness, protect fungal hosts from fungivorous predators, and enhance fungal virulence against plants, animals, and humans. These discoveries highlight the need for holistic investigations into bacterial-fungal endosymbiosis to fully understand their role in natural ecosystems. A deeper understanding of these multipartite partnerships offers exciting opportunities to improve ecosystem management, food safety, disease control, and crop productivity.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144513141","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}

{"title":"Hemolymph microbiota and host immunity of crustaceans and mollusks","authors":"Rohit Rathour, Yingxue Ma, Jinbo Xiong, Xian-Wei Wang, Jillian Petersen, Xinxu Zhang","doi":"10.1093/ismejo/wraf133","DOIUrl":"https://doi.org/10.1093/ismejo/wraf133","url":null,"abstract":"None declared.Conflicts of interestCrustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defence mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host’s immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unravelling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustaceans and mollusks species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"643 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503388","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}

{"title":"Syntrophic bacterial and host–microbe interactions in bacterial vaginosis","authors":"Elliot M Lee, Sujatha Srinivasan, Samuel O Purvine, Tina L Fiedler, Owen P Leiser, Sean C Proll, Samuel S Minot, Danijel Djukovic, Daniel Raftery, Christine Johnston, David N Fredricks, Brooke L Deatherage Kaiser","doi":"10.1093/ismejo/wraf055","DOIUrl":"https://doi.org/10.1093/ismejo/wraf055","url":null,"abstract":"Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host–bacteria and bacteria–bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144503378","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}